From 50ed96ff7377386faca081b201c6a4b02a9cb301 Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Wed, 5 Apr 2023 12:59:56 -0400 Subject: [PATCH 01/54] feat(URL): add param for initial series and sop uids to display (#3265) * feat: Allow navigating to a specified series and sop instance This was a feature in OHIF v2, so adding it to v3, albeit with new parameters. feat: Allow comma separated as well as repeated args params * docs * Test fixes * feat: Navigate to SOP selected - PR fixes * Updated docs * PR fixes --- .../default/src/DicomWebDataSource/index.js | 8 +-- ...taticWadoClient.js => StaticWadoClient.ts} | 51 ++++++++++++------- .../default/src/getHangingProtocolModule.js | 21 ++++++-- modes/basic-test-mode/src/index.js | 1 - platform/core/src/classes/ImageSet.js | 6 ++- .../HangingProtocolService.ts | 45 ++++++++++++++++ .../isDisplaySetFromUrl.ts | 46 +++++++++++++++++ platform/core/src/types/HangingProtocol.ts | 22 +++++--- platform/core/src/utils/index.js | 5 ++ platform/core/src/utils/index.test.js | 2 + platform/core/src/utils/splitComma.ts | 31 +++++++++++ platform/docs/docs/configuration/url.md | 39 ++++++++++++-- .../services/data/HangingProtocolService.md | 18 ++++++- .../customization/HangingProtocol.spec.js | 23 ++++++++- .../viewer/src/components/ViewportGrid.tsx | 7 +-- platform/viewer/src/routes/Mode/Mode.tsx | 6 ++- 16 files changed, 284 insertions(+), 47 deletions(-) rename extensions/default/src/DicomWebDataSource/utils/{StaticWadoClient.js => StaticWadoClient.ts} (79%) create mode 100644 platform/core/src/services/HangingProtocolService/isDisplaySetFromUrl.ts create mode 100644 platform/core/src/utils/splitComma.ts diff --git a/extensions/default/src/DicomWebDataSource/index.js b/extensions/default/src/DicomWebDataSource/index.js index 1af67936d..3534c727d 100644 --- a/extensions/default/src/DicomWebDataSource/index.js +++ b/extensions/default/src/DicomWebDataSource/index.js @@ -22,8 +22,8 @@ import { retrieveStudyMetadata, deleteStudyMetadataPromise, } from './retrieveStudyMetadata.js'; -import StaticWadoClient from './utils/StaticWadoClient.js'; -import getDirectURL from '../utils/getDirectURL.js'; +import StaticWadoClient from './utils/StaticWadoClient'; +import getDirectURL from '../utils/getDirectURL'; const { DicomMetaDictionary, DicomDict } = dcmjs.data; @@ -90,7 +90,9 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) { const implementation = { initialize: ({ params, query }) => { const { StudyInstanceUIDs: paramsStudyInstanceUIDs } = params; - const queryStudyInstanceUIDs = query.getAll('StudyInstanceUIDs'); + const queryStudyInstanceUIDs = utils.splitComma( + query.getAll('StudyInstanceUIDs') + ); const StudyInstanceUIDs = (queryStudyInstanceUIDs.length && queryStudyInstanceUIDs) || diff --git a/extensions/default/src/DicomWebDataSource/utils/StaticWadoClient.js b/extensions/default/src/DicomWebDataSource/utils/StaticWadoClient.ts similarity index 79% rename from extensions/default/src/DicomWebDataSource/utils/StaticWadoClient.js rename to extensions/default/src/DicomWebDataSource/utils/StaticWadoClient.ts index afe645cc2..9521e379b 100644 --- a/extensions/default/src/DicomWebDataSource/utils/StaticWadoClient.js +++ b/extensions/default/src/DicomWebDataSource/utils/StaticWadoClient.ts @@ -9,18 +9,19 @@ import { api } from 'dicomweb-client'; */ export default class StaticWadoClient extends api.DICOMwebClient { static studyFilterKeys = { - StudyInstanceUID: '0020000D', - PatientName: '00100010', + studyinstanceuid: '0020000D', + patientname: '00100010', '00100020': 'mrn', - StudyDescription: '00081030', - StudyDate: '00080020', - ModalitiesInStudy: '00080061', - AccessionNumber: '00080050', + studydescription: '00081030', + studydate: '00080020', + modalitiesinstudy: '00080061', + accessionnumber: '00080050', }; static seriesFilterKeys = { - SeriesInstanceUID: '0020000E', - SeriesNumber: '00200011', + seriesinstanceuid: '0020000E', + seriesnumber: '00200011', + modality: '00080060', }; constructor(qidoConfig) { @@ -37,15 +38,18 @@ export default class StaticWadoClient extends api.DICOMwebClient { async searchForStudies(options) { if (!this.staticWado) return super.searchForStudies(options); - let searchResult = await super.searchForStudies(options); + const searchResult = await super.searchForStudies(options); const { queryParams } = options; + if (!queryParams) return searchResult; + + const lowerParams = this.toLowerParams(queryParams); const filtered = searchResult.filter(study => { for (const key of Object.keys(StaticWadoClient.studyFilterKeys)) { if ( !this.filterItem( key, - queryParams, + lowerParams, study, StaticWadoClient.studyFilterKeys ) @@ -61,16 +65,18 @@ export default class StaticWadoClient extends api.DICOMwebClient { async searchForSeries(options) { if (!this.staticWado) return super.searchForSeries(options); - let searchResult = await super.searchForSeries(options); + const searchResult = await super.searchForSeries(options); const { queryParams } = options; if (!queryParams) return searchResult; - const filtered = searchResult.filter(study => { + const lowerParams = this.toLowerParams(queryParams); + + const filtered = searchResult.filter(series => { for (const key of Object.keys(StaticWadoClient.seriesFilterKeys)) { if ( !this.filterItem( key, - queryParams, - study, + lowerParams, + series, StaticWadoClient.seriesFilterKeys ) ) { @@ -136,13 +142,13 @@ export default class StaticWadoClient extends api.DICOMwebClient { /** * Filters the return list by the query parameters. * - * @param {*} key - * @param {*} queryParams + * @param anyCaseKey - a possible search key + * @param queryParams - * @param {*} study * @param {*} sourceFilterMap * @returns */ - filterItem(key, queryParams, study, sourceFilterMap) { + filterItem(key: string, queryParams, study, sourceFilterMap) { const altKey = sourceFilterMap[key] || key; if (!queryParams) return true; const testValue = queryParams[key] || queryParams[altKey]; @@ -153,6 +159,15 @@ export default class StaticWadoClient extends api.DICOMwebClient { return this.compareDateRange(testValue, valueElem.Value[0]); } const value = valueElem.Value; - return this.compareValues(testValue, value) && true; + return this.compareValues(testValue, value); + } + + /** Converts the query parameters to lower case query parameters */ + toLowerParams(queryParams: Record): Record { + const lowerParams = {}; + Object.entries(queryParams).forEach(([key, value]) => { + lowerParams[key.toLowerCase()] = value; + }); + return lowerParams; } } diff --git a/extensions/default/src/getHangingProtocolModule.js b/extensions/default/src/getHangingProtocolModule.js index a975a8968..b575d9086 100644 --- a/extensions/default/src/getHangingProtocolModule.js +++ b/extensions/default/src/getHangingProtocolModule.js @@ -7,7 +7,7 @@ const defaultProtocol = { hasUpdatedPriorsInformation: false, name: 'Default', createdDate: '2021-02-23T19:22:08.894Z', - modifiedDate: '2021-02-23T19:22:08.894Z', + modifiedDate: '2023-04-01', availableTo: {}, editableBy: {}, protocolMatchingRules: [], @@ -33,8 +33,6 @@ const defaultProtocol = { }, displaySetSelectors: { defaultDisplaySetId: { - // Unused currently - imageMatchingRules: [], // Matches displaysets, NOT series seriesMatchingRules: [ // Try to match series with images by default, to prevent weird display @@ -45,6 +43,15 @@ const defaultProtocol = { greaterThan: { value: 0 }, }, }, + // This display set will select the specified items by preference + // It has no affect if nothing is specified in the URL. + { + attribute: 'isDisplaySetFromUrl', + weight: 10, + constraint: { + equals: true, + }, + }, ], // Can be used to select matching studies // studyMatchingRules: [], @@ -65,7 +72,13 @@ const defaultProtocol = { viewportOptions: { viewportType: 'stack', toolGroupId: 'default', - // initialImageOptions: { + // This will specify the initial image options index if it matches in the URL + // and will otherwise not specify anything. + initialImageOptions: { + custom: 'sopInstanceLocation', + }, + // Other options for initialImageOptions, which can be included in the default + // custom attribute, or can be provided directly. // index: 180, // preset: 'middle', // 'first', 'last', 'middle' // }, diff --git a/modes/basic-test-mode/src/index.js b/modes/basic-test-mode/src/index.js index 11e06ec24..d465b7e09 100644 --- a/modes/basic-test-mode/src/index.js +++ b/modes/basic-test-mode/src/index.js @@ -133,7 +133,6 @@ function modeFactory() { const { toolGroupService, syncGroupService, - toolbarService, segmentationService, cornerstoneViewportService, } = servicesManager.services; diff --git a/platform/core/src/classes/ImageSet.js b/platform/core/src/classes/ImageSet.js index 9f4ba7074..80838c14f 100644 --- a/platform/core/src/classes/ImageSet.js +++ b/platform/core/src/classes/ImageSet.js @@ -30,6 +30,10 @@ class ImageSet { writable: false, value: guid(), // Unique ID of the instance }); + + this.instances = images; + this.instance = images[0]; + this.StudyInstanceUID = this.instance?.StudyInstanceUID; } getUID() { @@ -56,7 +60,7 @@ class ImageSet { } } - getNumImages = () => this.images.length + getNumImages = () => this.images.length; getImage(index) { return this.images[index]; diff --git a/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts b/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts index b366450d9..2d06acdaf 100644 --- a/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts +++ b/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts @@ -6,6 +6,10 @@ import IDisplaySet from '../DisplaySetService/IDisplaySet'; import { CommandsManager } from '../../classes'; import ServicesManager from '../ServicesManager'; import * as HangingProtocol from '../../types/HangingProtocol'; +import { + isDisplaySetFromUrl, + sopInstanceLocation, +} from './isDisplaySetFromUrl'; type Protocol = HangingProtocol.Protocol | HangingProtocol.ProtocolGenerator; @@ -81,6 +85,14 @@ export default class HangingProtocolService extends PubSubService { // we can add more advanced checking here callback: displaySet => displaySet.isReconstructable ?? false, }, + isDisplaySetFromUrl: { + name: 'Checks if the display set is as specified in the URL', + callback: isDisplaySetFromUrl, + }, + sopInstanceLocation: { + name: 'Gets the position of the specified sop instance', + callback: sopInstanceLocation, + }, }; listeners = {}; registeredImageLoadStrategies = {}; @@ -648,6 +660,39 @@ export default class HangingProtocolService extends PubSubService { return viewportsToUpdate; } + /** + * Gets a computed options value, or a copy of the options + * This allows computing values such as the initial image index to use + * based on custom attribute functions, the same as the validators. + * Computing individual values is something that can be declared statically + * as long as the named functions are provided ahead of time, which is much + * simpler than recomputing the entire protocol. + */ + public getComputedOptions( + options: Record, + displaySetUIDs: string[] + ) { + const computed = { ...options }; + let displaySets; + for (const key in computed) { + const value = computed[key]; + if (!value) continue; + if (value.custom) { + if (!displaySets) { + displaySets = this.displaySets.filter( + displaySet => + displaySetUIDs.indexOf(displaySet.displaySetInstanceUID) !== -1 + ); + } + computed[key] = this.customAttributeRetrievalCallbacks[ + value.custom + ].callback.call(computed, displaySets); + if (computed[key] === undefined) computed[key] = computed.defaultValue; + } + } + return computed; + } + /** * It applied the protocol to the current studies and display sets based on the * protocolId that is provided. diff --git a/platform/core/src/services/HangingProtocolService/isDisplaySetFromUrl.ts b/platform/core/src/services/HangingProtocolService/isDisplaySetFromUrl.ts new file mode 100644 index 000000000..a271d5ecd --- /dev/null +++ b/platform/core/src/services/HangingProtocolService/isDisplaySetFromUrl.ts @@ -0,0 +1,46 @@ +import { getSplitParam } from '../../utils'; + +/** Indicates if the given display set is the one specified in the + * displaySet parameter in the URL + * The parameters are: + * initialSeriesInstanceUID + * initialSOPInstanceUID + */ +const isDisplaySetFromUrl = (displaySet): boolean => { + const params = new URLSearchParams(window.location.search); + const initialSeriesInstanceUID = getSplitParam( + 'initialseriesinstanceuid', + params + ); + const initialSOPInstanceUID = getSplitParam('initialsopinstanceuid', params); + if (!initialSeriesInstanceUID && !initialSOPInstanceUID) return false; + const isSeriesMatch = + !initialSeriesInstanceUID || + initialSeriesInstanceUID.some( + seriesUID => displaySet.SeriesInstanceUID === seriesUID + ); + const isSopMatch = + !initialSOPInstanceUID || + displaySet.instances?.some?.(instance => + initialSOPInstanceUID.some(sopUID => sopUID === instance.SOPInstanceUID) + ); + return isSeriesMatch && isSopMatch; +}; + +/** Returns the index location of the requested image, or the defaultValue in this. + * Returns undefined to fallback to the defaultValue + */ +function sopInstanceLocation(displaySets) { + const displaySet = displaySets[0]; + if (!displaySet) return; + const initialSOPInstanceUID = getSplitParam('initialsopinstanceuid'); + if (!initialSOPInstanceUID) return; + + const index = displaySet.instances.findIndex(instance => + initialSOPInstanceUID.includes(instance.SOPInstanceUID) + ); + // Need to return in the initial position specified format. + return index === -1 ? undefined : { index }; +} + +export { isDisplaySetFromUrl, sopInstanceLocation }; diff --git a/platform/core/src/types/HangingProtocol.ts b/platform/core/src/types/HangingProtocol.ts index 5cb26e20c..fec29f489 100644 --- a/platform/core/src/types/HangingProtocol.ts +++ b/platform/core/src/types/HangingProtocol.ts @@ -70,8 +70,8 @@ export type ConstraintValue = | boolean | [] | { - value: string | number | boolean | []; - }; + value: string | number | boolean | []; + }; export type Constraint = { // This value exactly @@ -135,19 +135,27 @@ export type SyncGroup = { target?: boolean; }; +/** Declares a custom option, that is a computed type value */ +export type CustomOptionAttribute = { + custom: string; + defaultValue?: T; +}; + +export type CustomOption = CustomOptionAttribute | T; + export type initialImageOptions = { index?: number; preset?: string; // todo: type more }; export type ViewportOptions = { - toolGroupId?: string; - viewportType?: string; + toolGroupId?: CustomOption; + viewportType?: CustomOption; id?: string; - orientation?: string; + orientation?: CustomOption; viewportId?: string; - initialImageOptions?: initialImageOptions; - syncGroups?: SyncGroup[]; + initialImageOptions?: CustomOption; + syncGroups?: CustomOption[]; customViewportProps?: Record; // Set to true to allow non-matching drag and drop or options provided // from options.displaySetSelectorsMap diff --git a/platform/core/src/utils/index.js b/platform/core/src/utils/index.js index 4c54c32ef..06e7537f3 100644 --- a/platform/core/src/utils/index.js +++ b/platform/core/src/utils/index.js @@ -33,6 +33,7 @@ import { seriesSortCriteria, } from './sortStudy'; import { subscribeToNextViewportGridChange } from './subscribeToNextViewportGridChange'; +import { splitComma, getSplitParam } from './splitComma'; // Commented out unused functionality. // Need to implement new mechanism for derived displaySets using the displaySetManager. @@ -71,6 +72,8 @@ const utils = { roundNumber, downloadCSVReport, subscribeToNextViewportGridChange, + splitComma, + getSplitParam, }; export { @@ -100,6 +103,8 @@ export { debounce, roundNumber, downloadCSVReport, + splitComma, + getSplitParam, }; export default utils; diff --git a/platform/core/src/utils/index.test.js b/platform/core/src/utils/index.test.js index cae769191..b3c3e1e26 100644 --- a/platform/core/src/utils/index.test.js +++ b/platform/core/src/utils/index.test.js @@ -13,6 +13,8 @@ describe('Top level exports', () => { 'sortStudyInstances', 'sortStudySeries', 'sortingCriteria', + 'splitComma', + 'getSplitParam', 'isLowPriorityModality', 'writeScript', 'debounce', diff --git a/platform/core/src/utils/splitComma.ts b/platform/core/src/utils/splitComma.ts new file mode 100644 index 000000000..e8aab0b47 --- /dev/null +++ b/platform/core/src/utils/splitComma.ts @@ -0,0 +1,31 @@ +/** Splits a list of stirngs by commas within the strings */ +const splitComma = (strings: string[]): string[] => { + if (!strings) return null; + for (let i = 0; i < strings.length; i++) { + const comma = strings[i].indexOf(','); + if (comma !== -1) { + const splits = strings[i].split(/,/); + strings.splice(i, 1, ...splits); + } + } + return strings; +}; + +/** + * Returns an array of the comma split parameters from the given URL search params + * @param lowerCaseKey - lower case search parameter value + * @param params - URLSearchParams + * @returns Array of comma split items matching, or null + */ +const getSplitParam = ( + lowerCaseKey: string, + params = new URLSearchParams(window.location.search) +): string[] => { + return splitComma( + [...params] + .find(([key, value]) => key.toLowerCase() === lowerCaseKey && value) + ?.slice?.(1) + ); +}; + +export { splitComma, getSplitParam }; diff --git a/platform/docs/docs/configuration/url.md b/platform/docs/docs/configuration/url.md index f0e12ff36..a4ec17580 100644 --- a/platform/docs/docs/configuration/url.md +++ b/platform/docs/docs/configuration/url.md @@ -110,17 +110,46 @@ You can open more than one study in the Viewer by adding the `StudyInstanceUIDs` :::tip You can ues this feature to open a current and prior study in the Viewer. -Read more in the [Hanging Protocol Module](../platform/extensions/modules/hpModule.md#matching-on-prior-study-with-uid) section +Read more in the [Hanging Protocol Module](../platform/extensions/modules/hpModule.md#matching-on-prior-study-with-uid) section. You can also use commas to separate +values. ::: -### SeriesInstanceUIDs +### SeriesInstanceUID and initialSeriesInstanceUID -Sometimes you need to only open a specific series in a study, you can do that by +Sometimes you need to only retrieve a specific series in a study, you can do +that by providing series level QIDO query parameters in the URL such as +SeriesInstanceUID or SeriesNumber. This does NOT work with instance or study +level parameters. For example: ```js -/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125095722.1&SeriesInstanceUID=1.3.6.1.4.1.25403.345050719074.3824.20170125095748.1 +http://localhost:3000/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1&SeriesInstanceUID=1.3.6.1.4.1.25403.345050719074.3824.20170125113545.4 ``` -This will only open the viewer with one series (one displaySet). +This will only open the viewer with one series (one displaySet) loaded, and no +queries made for any other series. + +Alternatively, sometimes you want to just open the study on a specified series +and/or display a particular sop instance, which you can accomplish using: +`initialSeriesInstanceUID` and/or `initialSOPInstanceUID` +to select the series to open on, but allowing other +series to be present in the study browser panel. This is the same behaviour +as in OHIF 2.0, albeit on different URL parameters. For example: + +```js +http://localhost:3000/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1&initialSeriesInstanceUID=1.3.6.1.4.1.25403.345050719074.3824.20170125113545.4 +``` + +Note that you can combine these, if you want to load a specific set of series +plus show an initial one as the first one selected, for example: + +```js +http://localhost:3000/viewer?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1&SeriesInstanceUID=1.3.6.1.4.1.25403.345050719074.3824.20170125113545.4&initialSopInstanceUID=1.3.6.1.4.1.25403.345050719074.3824.20170125113546.1 +``` + +### hangingProtocolId + +You can select the initial hanging protocol to apply by using the +hangingProtocolId parameter. The selected parameter must be available in a +hangingProtocolModule registration, but does not have to be active. diff --git a/platform/docs/docs/platform/services/data/HangingProtocolService.md b/platform/docs/docs/platform/services/data/HangingProtocolService.md index 71dc86f49..21f615824 100644 --- a/platform/docs/docs/platform/services/data/HangingProtocolService.md +++ b/platform/docs/docs/platform/services/data/HangingProtocolService.md @@ -218,7 +218,8 @@ the display set is the same as the other viewports, but the from the display set selector which isn't already filling a view. ## Custom Attribute -In some situations, you might want to match based on a custom attribute and not the DICOM tags. For instance, +In some situations, you might want to match based on a custom +attribute and not the DICOM tags. For instance, if you have assigned a `timepointId` to each study, and you want to match based on it. Good news is that, in `OHIF-v3` you can define you custom attribute and use it for matching. @@ -294,3 +295,18 @@ function modeFactory() { }; } ``` + +### Custom Attributes for Viewport Options + +The custom attributes can also be used for viewport options. This example, +from the default hanging protocol navigates the image to the image +specified in the URL: + +```javascript +viewportOptions: { + initialImageOptions: { + // custom attribute name is selected by 'custom' + custom: 'sopInstanceLocation', + // This is the value returned if the above doesn't return anything + defaultValue: { index: 5 }, +``` diff --git a/platform/viewer/cypress/integration/customization/HangingProtocol.spec.js b/platform/viewer/cypress/integration/customization/HangingProtocol.spec.js index c7b8a8417..6d3f87384 100644 --- a/platform/viewer/cypress/integration/customization/HangingProtocol.spec.js +++ b/platform/viewer/cypress/integration/customization/HangingProtocol.spec.js @@ -1,5 +1,5 @@ describe('OHIF HP', () => { - beforeEach(() => { + const beforeSetup = () => { cy.checkStudyRouteInViewer( '1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1', '&hangingProtocolId=@ohif/hp-extension.mn' @@ -7,15 +7,19 @@ describe('OHIF HP', () => { cy.expectMinimumThumbnails(3); cy.initCornerstoneToolsAliases(); cy.initCommonElementsAliases(); - }); + }; it('Should display 3 up', () => { + beforeSetup(); + cy.get('[data-cy="viewport-pane"]') .its('length') .should('be.eq', 3); }); it('Should navigate next/previous stage', () => { + beforeSetup(); + cy.get('body').type(','); cy.wait(250); cy.get('[data-cy="viewport-pane"]') @@ -28,4 +32,19 @@ describe('OHIF HP', () => { .its('length') .should('be.eq', 2); }); + + it('Should navigate to display set specified', () => { + // This filters by series instance UID, meaning there will only be 1 thumbnail + // It applies the initial SOP instance, navigating to that image + cy.checkStudyRouteInViewer( + '1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1', + '&SeriesInstanceUID=1.3.6.1.4.1.25403.345050719074.3824.20170125113545.4&initialSopInstanceUID=1.3.6.1.4.1.25403.345050719074.3824.20170125113546.1' + ); + cy.expectMinimumThumbnails(1); + cy.initCornerstoneToolsAliases(); + cy.initCommonElementsAliases(); + + // The specified series/sop UID's are index 101, so ensure that image is displayed + cy.get('@viewportInfoTopRight').should('contains.text', 'I:6'); + }); }); diff --git a/platform/viewer/src/components/ViewportGrid.tsx b/platform/viewer/src/components/ViewportGrid.tsx index 2eea5be09..03970597c 100644 --- a/platform/viewer/src/components/ViewportGrid.tsx +++ b/platform/viewer/src/components/ViewportGrid.tsx @@ -99,9 +99,10 @@ function ViewerViewportGrid(props) { return { displaySetInstanceUIDs: displaySetUIDsToHang, displaySetOptions: displaySetUIDsToHangOptions, - viewportOptions: { - ...viewportOptions, - }, + viewportOptions: hangingProtocolService.getComputedOptions( + viewportOptions, + displaySetUIDsToHang + ), }; }; diff --git a/platform/viewer/src/routes/Mode/Mode.tsx b/platform/viewer/src/routes/Mode/Mode.tsx index a48f05500..e0eb6d46e 100644 --- a/platform/viewer/src/routes/Mode/Mode.tsx +++ b/platform/viewer/src/routes/Mode/Mode.tsx @@ -279,8 +279,10 @@ export default function ModeRoute({ const filters = Array.from(query.keys()).reduce( (acc: Record, val: string) => { - if (val !== 'StudyInstanceUIDs') { - if (['seriesInstanceUID', 'SeriesInstanceUID'].includes(val)) { + const lowerVal = val.toLowerCase(); + if (lowerVal !== 'studyinstanceuids') { + // Not sure why the case matters here - it doesn't in the URL + if (lowerVal === 'seriesinstanceuid') { return { ...acc, seriesInstanceUID: query.get(val), From af50815ebbeef5dca97493ffa24339db64e33139 Mon Sep 17 00:00:00 2001 From: Ouwen Huang Date: Wed, 5 Apr 2023 14:29:20 -0400 Subject: [PATCH 02/54] fix(crosshairs): suppressed error for crosshair (#3237) --- .../cornerstone/src/initMeasurementService.js | 14 ++++++++++++++ .../CornerstoneCacheService.ts | 1 + 2 files changed, 15 insertions(+) diff --git a/extensions/cornerstone/src/initMeasurementService.js b/extensions/cornerstone/src/initMeasurementService.js index 93a618eaf..36b7229d2 100644 --- a/extensions/cornerstone/src/initMeasurementService.js +++ b/extensions/cornerstone/src/initMeasurementService.js @@ -48,6 +48,20 @@ const initMeasurementService = ( Length.toMeasurement ); + measurementService.addMapping( + csTools3DVer1MeasurementSource, + 'Crosshairs', + Length.matchingCriteria, + () => { + console.warn('Crosshairs mapping not implemented.'); + return {}; + }, + () => { + console.warn('Crosshairs mapping not implemented.'); + return {}; + } + ); + measurementService.addMapping( csTools3DVer1MeasurementSource, 'Bidirectional', diff --git a/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts b/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts index 8a29bcab4..56c8d6fa5 100644 --- a/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts +++ b/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts @@ -100,6 +100,7 @@ class CornerstoneCacheService { if (volume) { cs3DCache.removeVolumeLoadObject(volumeId); + this.volumeImageIds.delete(volumeId); } const displaySets = viewportData.data.map(({ displaySetInstanceUID }) => From b5aa5df575e77ecc8c6dc94659da63f81fd13bf2 Mon Sep 17 00:00:00 2001 From: Ibrahim <93064150+IbrahimCSAE@users.noreply.github.com> Date: Wed, 5 Apr 2023 16:39:09 -0230 Subject: [PATCH 03/54] fix(SRTool): Ellipse Display for DICOMSR Tool (#3307) --- .../src/tools/DICOMSRDisplayTool.ts | 21 +++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/extensions/cornerstone-dicom-sr/src/tools/DICOMSRDisplayTool.ts b/extensions/cornerstone-dicom-sr/src/tools/DICOMSRDisplayTool.ts index 9c4f3c2ea..347159d20 100644 --- a/extensions/cornerstone-dicom-sr/src/tools/DICOMSRDisplayTool.ts +++ b/extensions/cornerstone-dicom-sr/src/tools/DICOMSRDisplayTool.ts @@ -307,13 +307,26 @@ export default class DICOMSRDisplayTool extends AnnotationTool { const ellipsePointsWorld = data; + const rotation = viewport.getRotation(); + canvasCoordinates = ellipsePointsWorld.map(p => viewport.worldToCanvas(p) ); - - const canvasCorners = >( - utilities.math.ellipse.getCanvasEllipseCorners(canvasCoordinates) - ); + let canvasCorners; + if (rotation == 90 || rotation == 270) { + canvasCorners = >( + utilities.math.ellipse.getCanvasEllipseCorners([ + canvasCoordinates[2], + canvasCoordinates[3], + canvasCoordinates[0], + canvasCoordinates[1], + ]) + ); + } else { + canvasCorners = >( + utilities.math.ellipse.getCanvasEllipseCorners(canvasCoordinates) + ); + } const lineUID = `${index}`; drawing.drawEllipse( From 25b4f8ed97fc4381a48c58406fe317b0ffbeb0ea Mon Sep 17 00:00:00 2001 From: Mateus Freira dos Santos Date: Wed, 5 Apr 2023 17:20:14 -0300 Subject: [PATCH 04/54] feat(App): support async config function (#3313) --- platform/viewer/src/appInit.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/platform/viewer/src/appInit.js b/platform/viewer/src/appInit.js index 3fd86e1ce..58908c374 100644 --- a/platform/viewer/src/appInit.js +++ b/platform/viewer/src/appInit.js @@ -36,7 +36,7 @@ async function appInit(appConfigOrFunc, defaultExtensions, defaultModes) { const appConfig = { ...(typeof appConfigOrFunc === 'function' - ? appConfigOrFunc({ servicesManager }) + ? await appConfigOrFunc({ servicesManager }) : appConfigOrFunc), }; From 45a34ae0fef744be1bff0c72360069238255da0c Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Wed, 5 Apr 2023 16:37:37 -0400 Subject: [PATCH 05/54] fix(URL): allow multi filter query (#3314) --- platform/core/src/utils/splitComma.ts | 8 ++++---- platform/viewer/src/routes/Mode/Mode.tsx | 10 ++++++---- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/platform/core/src/utils/splitComma.ts b/platform/core/src/utils/splitComma.ts index e8aab0b47..4354e0ce0 100644 --- a/platform/core/src/utils/splitComma.ts +++ b/platform/core/src/utils/splitComma.ts @@ -21,11 +21,11 @@ const getSplitParam = ( lowerCaseKey: string, params = new URLSearchParams(window.location.search) ): string[] => { - return splitComma( - [...params] - .find(([key, value]) => key.toLowerCase() === lowerCaseKey && value) - ?.slice?.(1) + const sourceKey = [...params.keys()].find( + it => it.toLowerCase() === lowerCaseKey ); + if (!sourceKey) return; + return splitComma(params.getAll(sourceKey)); }; export { splitComma, getSplitParam }; diff --git a/platform/viewer/src/routes/Mode/Mode.tsx b/platform/viewer/src/routes/Mode/Mode.tsx index e0eb6d46e..7b06bf445 100644 --- a/platform/viewer/src/routes/Mode/Mode.tsx +++ b/platform/viewer/src/routes/Mode/Mode.tsx @@ -1,15 +1,16 @@ import React, { useEffect, useState, useRef } from 'react'; import { useParams, useLocation } from 'react-router'; - import PropTypes from 'prop-types'; // TODO: DicomMetadataStore should be injected? -import { DicomMetadataStore, ServicesManager } from '@ohif/core'; +import { DicomMetadataStore, ServicesManager, utils } from '@ohif/core'; import { DragAndDropProvider, ImageViewerProvider } from '@ohif/ui'; import { useQuery, useSearchParams } from '@hooks'; import ViewportGrid from '@components/ViewportGrid'; import Compose from './Compose'; import getStudies from './studiesList'; +const { getSplitParam } = utils; + /** * Initialize the route. * @@ -283,13 +284,14 @@ export default function ModeRoute({ if (lowerVal !== 'studyinstanceuids') { // Not sure why the case matters here - it doesn't in the URL if (lowerVal === 'seriesinstanceuid') { + const seriesUIDs = getSplitParam(lowerVal, query); return { ...acc, - seriesInstanceUID: query.get(val), + seriesInstanceUID: seriesUIDs, }; } - return { ...acc, [val]: query.get(val) }; + return { ...acc, [val]: getSplitParam(lowerVal, query) }; } }, {} From d3da969d23584dbbc5c8eca9a498d378cea595f6 Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Wed, 5 Apr 2023 17:26:51 -0400 Subject: [PATCH 06/54] fix(viewport): Initial blank image on SR/SEG initial display (#3304) * fix: Blank display area on initial DICOM SR load * Docs * Fix a NPE --- .../src/getHangingProtocolModule.ts | 78 +++++++++++++++++++ extensions/cornerstone-dicom-sr/src/index.tsx | 26 +++---- .../src/Viewport/OHIFCornerstoneViewport.tsx | 5 +- .../viewer/src/components/ViewportGrid.tsx | 5 +- 4 files changed, 97 insertions(+), 17 deletions(-) create mode 100644 extensions/cornerstone-dicom-sr/src/getHangingProtocolModule.ts diff --git a/extensions/cornerstone-dicom-sr/src/getHangingProtocolModule.ts b/extensions/cornerstone-dicom-sr/src/getHangingProtocolModule.ts new file mode 100644 index 000000000..e9fcf31be --- /dev/null +++ b/extensions/cornerstone-dicom-sr/src/getHangingProtocolModule.ts @@ -0,0 +1,78 @@ +import { Types } from '@ohif/core'; + +const srProtocol: Types.HangingProtocol.Protocol = { + id: '@ohif/sr', + // Don't store this hanging protocol as it applies to the currently active + // display set by default + // cacheId: null, + hasUpdatedPriorsInformation: false, + name: 'SR Key Images', + // Just apply this one when specifically listed + protocolMatchingRules: [], + toolGroupIds: ['default'], + // -1 would be used to indicate active only, whereas other values are + // the number of required priors referenced - so 0 means active with + // 0 or more priors. + numberOfPriorsReferenced: 0, + // Default viewport is used to define the viewport when + // additional viewports are added using the layout tool + defaultViewport: { + viewportOptions: { + viewportType: 'stack', + toolGroupId: 'default', + allowUnmatchedView: true, + }, + displaySets: [ + { + id: 'srDisplaySetId', + matchedDisplaySetsIndex: -1, + }, + ], + }, + displaySetSelectors: { + srDisplaySetId: { + seriesMatchingRules: [ + { + attribute: 'Modality', + constraint: { + equals: 'SR', + }, + }, + ], + }, + }, + stages: [ + { + name: 'SR Key Images', + viewportStructure: { + layoutType: 'grid', + properties: { + rows: 1, + columns: 1, + }, + }, + viewports: [ + { + viewportOptions: { allowUnmatchedView: true }, + displaySets: [ + { + id: 'srDisplaySetId', + }, + ], + }, + ], + }, + ], +}; + +function getHangingProtocolModule() { + return [ + { + name: srProtocol.id, + protocol: srProtocol, + }, + ]; +} + +export default getHangingProtocolModule; +export { srProtocol }; diff --git a/extensions/cornerstone-dicom-sr/src/index.tsx b/extensions/cornerstone-dicom-sr/src/index.tsx index bab79924a..53d1217e7 100644 --- a/extensions/cornerstone-dicom-sr/src/index.tsx +++ b/extensions/cornerstone-dicom-sr/src/index.tsx @@ -1,8 +1,11 @@ import React from 'react'; import getSopClassHandlerModule from './getSopClassHandlerModule'; +import getHangingProtocolModule, { + srProtocol, +} from './getHangingProtocolModule'; import onModeEnter from './onModeEnter'; -import commandsModule from './commandsModule'; -import init from './init'; +import getCommandsModule from './commandsModule'; +import preRegistration from './init'; import { id } from './id.js'; import toolNames from './tools/toolNames'; import hydrateStructuredReport from './utils/hydrateStructuredReport'; @@ -31,9 +34,7 @@ const dicomSRExtension = { id, onModeEnter, - preRegistration({ servicesManager, configuration = {} }) { - init({ servicesManager, configuration }); - }, + preRegistration, /** * @@ -54,14 +55,11 @@ const dicomSRExtension = { return [{ name: 'dicom-sr', component: ExtendedOHIFCornerstoneSRViewport }]; }, - getCommandsModule({ servicesManager, commandsManager, extensionManager }) { - return commandsModule({ - servicesManager, - commandsManager, - extensionManager, - }); - }, + getCommandsModule, getSopClassHandlerModule, + getHangingProtocolModule, + + // Include dynmically computed values such as toolNames not known till instantiation getUtilityModule({ servicesManager }) { return [ { @@ -75,4 +73,6 @@ const dicomSRExtension = { }; export default dicomSRExtension; -export { hydrateStructuredReport }; + +// Put static exports here so they can be type checked +export { hydrateStructuredReport, srProtocol }; diff --git a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx index 83d012ef2..fb51ccdd6 100644 --- a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx +++ b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx @@ -390,8 +390,9 @@ const OHIFCornerstoneViewport = React.memo(props => { initialImageIndex ); - storePresentation(); - + // The presentation state will have been stored previously by closing + // a viewport. Otherwise, this viewport will be unchanged and the + // presentation information will be directly carried over. const { lutPresentationStore, positionPresentationStore, diff --git a/platform/viewer/src/components/ViewportGrid.tsx b/platform/viewer/src/components/ViewportGrid.tsx index 03970597c..ca2cc71cc 100644 --- a/platform/viewer/src/components/ViewportGrid.tsx +++ b/platform/viewer/src/components/ViewportGrid.tsx @@ -200,11 +200,12 @@ function ViewerViewportGrid(props) { } updatedViewports.forEach(vp => { + vp.viewportOptions ||= {}; const { orientation, viewportType } = vp.viewportOptions; let initialImageOptions; // For initial imageIndex to hang be careful for the volume viewport - if (viewportType === 'stack') { + if (viewportType === 'stack' || !viewportType) { initialImageOptions = { index: imageIndex, }; @@ -227,7 +228,7 @@ function ViewerViewportGrid(props) { } } - vp.viewportOptions['initialImageOptions'] = initialImageOptions; + vp.viewportOptions.initialImageOptions = initialImageOptions; }); viewportGridService.setDisplaySetsForViewports(updatedViewports); From 1173e7de6ca06e1e5895e9c649bc6bafac38d902 Mon Sep 17 00:00:00 2001 From: dxlin Date: Thu, 6 Apr 2023 14:05:46 -0400 Subject: [PATCH 07/54] fix(ROIThreshold): fix setWeight not updating properly for ROIThreshold panel (#3315) --- .../ROIThresholdConfiguration.tsx | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/ROIThresholdConfiguration.tsx b/extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/ROIThresholdConfiguration.tsx index cd55a3cb0..1a2b706f8 100644 --- a/extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/ROIThresholdConfiguration.tsx +++ b/extensions/tmtv/src/Panels/PanelROIThresholdSegmentation/ROIThresholdConfiguration.tsx @@ -72,7 +72,9 @@ function ROIThresholdConfiguration({ config, dispatch, runCommand }) { onChange={e => { dispatch({ type: 'setWeight', - payload: e.target.value, + payload: { + weight: e.target.value, + }, }); }} /> From 83b460635794f962f1cf6978eaecc4f74073d03f Mon Sep 17 00:00:00 2001 From: Sofien-Sellami <73444179+Sofien-Sellami@users.noreply.github.com> Date: Fri, 14 Apr 2023 04:08:13 +0100 Subject: [PATCH 08/54] fix(hp): Add displaySetMatchDetails and displaySets to options in (#3320) The sameAs function requires displaySetMatchDetails and displaySets to compare attributes between display sets, but these properties were not being passed into the options object. This commit adds the necessary lines of code to include displaySetMatchDetails and displaySets in the options object, fixing the issue where the custom attribute function 'sameAs' was missing required data. --- .../HangingProtocolService.ts | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts b/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts index 2d06acdaf..4ae568c2a 100644 --- a/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts +++ b/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts @@ -1297,7 +1297,11 @@ export default class HangingProtocolService extends PubSubService { const studyMatchDetails = this.protocolEngine.findMatch( study, studyMatchingRules, - { studies: this.studies, displaySets: studyDisplaySets } + { + studies: this.studies, + displaySets: studyDisplaySets, + displaySetMatchDetails: this.displaySetMatchDetails, + } ); // Prevent bestMatch from being updated if the matchDetails' required attribute check has failed @@ -1321,7 +1325,12 @@ export default class HangingProtocolService extends PubSubService { displaySet, seriesMatchingRules, // Todo: why we have images here since the matching type does not have it - { studies: this.studies, instance: displaySet.images?.[0] } + { + studies: this.studies, + instance: displaySet.images?.[0], + displaySetMatchDetails: this.displaySetMatchDetails, + displaySets: studyDisplaySets, + } ); // Prevent bestMatch from being updated if the matchDetails' required attribute check has failed From 47c25f4364bf76babe5ab99b4a2535a60703f66f Mon Sep 17 00:00:00 2001 From: "M.D" <26860200+md-prog@users.noreply.github.com> Date: Mon, 17 Apr 2023 08:23:03 -0400 Subject: [PATCH 09/54] feat(measurements): add CircleROI Tool (#3211) * [refactor] measurement service mapping files - rename to .ts files * [fix] RectangleROI - measurement service mapping _getReport() function - tool name fix * [feat] added CircleROI tool from updated cornerstone3D * [refactor] fix for typescript strong typing warnings * [feat] cornerstone-dicom-sr extension - added CircleROI tool * [feat] added toolbar button for CircleROI tool * [doc] doc updates for CircleROI tool * [update] library - dcmjs to 0.29.5 * [fix] roundNumber() function when given strings * [fix] refactor after upgrading conerstonejs library 0.49.0 * yarn.lock file change --- extensions/cornerstone-dicom-sr/package.json | 2 +- extensions/cornerstone-dicom-sr/src/init.ts | 3 + .../src/tools/toolNames.ts | 1 + extensions/cornerstone/package.json | 2 +- .../cornerstone/src/initCornerstoneTools.js | 3 + .../cornerstone/src/initMeasurementService.js | 9 + .../{ArrowAnnotate.js => ArrowAnnotate.ts} | 0 .../{Bidirectional.js => Bidirectional.ts} | 0 .../measurementServiceMappings/CircleROI.ts | 228 ++++++++++++++++++ .../{EllipticalROI.js => EllipticalROI.ts} | 0 .../{Length.js => Length.ts} | 32 +-- .../RectangleROI.ts | 26 +- .../constants/supportedTools.js | 1 + .../measurementServiceMappingsFactory.ts | 19 ++ .../utils/getSOPInstanceAttributes.js | 4 +- extensions/default/package.json | 2 +- extensions/dicom-pdf/package.json | 2 +- extensions/dicom-video/package.json | 2 +- extensions/measurement-tracking/package.json | 2 +- extensions/tmtv/package.json | 2 +- modes/basic-dev-mode/src/index.js | 8 +- modes/basic-dev-mode/src/toolbarButtons.js | 15 ++ modes/basic-test-mode/src/initToolGroups.js | 3 + modes/basic-test-mode/src/toolbarButtons.js | 23 ++ modes/longitudinal/src/initToolGroups.js | 3 + modes/longitudinal/src/toolbarButtons.js | 23 ++ modes/tmtv/src/toolbarButtons.js | 17 +- platform/core/package.json | 2 +- platform/core/src/utils/roundNumber.js | 6 +- .../platform/extensions/modules/toolbar.md | 10 + .../platform/services/data/ToolbarService.md | 10 + platform/ui/src/assets/icons/tool-circle.svg | 3 + platform/ui/src/components/Icon/getIcon.js | 2 + platform/viewer/package.json | 2 +- yarn.lock | 14 +- 35 files changed, 412 insertions(+), 69 deletions(-) rename extensions/cornerstone/src/utils/measurementServiceMappings/{ArrowAnnotate.js => ArrowAnnotate.ts} (100%) rename extensions/cornerstone/src/utils/measurementServiceMappings/{Bidirectional.js => Bidirectional.ts} (100%) create mode 100644 extensions/cornerstone/src/utils/measurementServiceMappings/CircleROI.ts rename extensions/cornerstone/src/utils/measurementServiceMappings/{EllipticalROI.js => EllipticalROI.ts} (100%) rename extensions/cornerstone/src/utils/measurementServiceMappings/{Length.js => Length.ts} (90%) create mode 100644 platform/ui/src/assets/icons/tool-circle.svg diff --git a/extensions/cornerstone-dicom-sr/package.json b/extensions/cornerstone-dicom-sr/package.json index 923385eda..76e8fe82b 100644 --- a/extensions/cornerstone-dicom-sr/package.json +++ b/extensions/cornerstone-dicom-sr/package.json @@ -36,7 +36,7 @@ "@ohif/extension-cornerstone": "^3.0.0", "@ohif/extension-measurement-tracking": "^3.0.0", "@ohif/ui": "^2.0.0", - "dcmjs": "^0.29.4", + "dcmjs": "^0.29.5", "dicom-parser": "^1.8.9", "hammerjs": "^2.0.8", "prop-types": "^15.6.2", diff --git a/extensions/cornerstone-dicom-sr/src/init.ts b/extensions/cornerstone-dicom-sr/src/init.ts index ec24b5c48..84cbcaf37 100644 --- a/extensions/cornerstone-dicom-sr/src/init.ts +++ b/extensions/cornerstone-dicom-sr/src/init.ts @@ -6,6 +6,7 @@ import { BidirectionalTool, CobbAngleTool, EllipticalROITool, + CircleROITool, LengthTool, PlanarFreehandROITool, } from '@cornerstonejs/tools'; @@ -24,6 +25,7 @@ export default function init({ addToolInstance(toolNames.SRLength, LengthTool, {}); addToolInstance(toolNames.SRBidirectional, BidirectionalTool); addToolInstance(toolNames.SREllipticalROI, EllipticalROITool); + addToolInstance(toolNames.SRCircleROI, CircleROITool); addToolInstance(toolNames.SRArrowAnnotate, ArrowAnnotateTool); addToolInstance(toolNames.SRAngle, AngleTool); // TODO - fix the SR display of Cobb Angle, as it joins the two lines @@ -40,6 +42,7 @@ export default function init({ SRLength: dashedLine, SRBidirectional: dashedLine, SREllipticalROI: dashedLine, + SRCircleROI: dashedLine, SRArrowAnnotate: dashedLine, SRCobbAngle: dashedLine, SRAngle: dashedLine, diff --git a/extensions/cornerstone-dicom-sr/src/tools/toolNames.ts b/extensions/cornerstone-dicom-sr/src/tools/toolNames.ts index 48375f4cb..2e52ec111 100644 --- a/extensions/cornerstone-dicom-sr/src/tools/toolNames.ts +++ b/extensions/cornerstone-dicom-sr/src/tools/toolNames.ts @@ -5,6 +5,7 @@ const toolNames = { SRLength: 'SRLength', SRBidirectional: 'SRBidirectional', SREllipticalROI: 'SREllipticalROI', + SRCircleROI: 'SRCircleROI', SRArrowAnnotate: 'SRArrowAnnotate', SRAngle: 'SRAngle', SRCobbAngle: 'SRCobbAngle', diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json index 2eab62700..cae1befd0 100644 --- a/extensions/cornerstone/package.json +++ b/extensions/cornerstone/package.json @@ -30,7 +30,7 @@ "@ohif/core": "^3.0.0", "@ohif/ui": "^2.0.0", "cornerstone-wado-image-loader": "^4.13.0", - "dcmjs": "^0.29.4", + "dcmjs": "^0.29.5", "dicom-parser": "^1.8.9", "hammerjs": "^2.0.8", "prop-types": "^15.6.2", diff --git a/extensions/cornerstone/src/initCornerstoneTools.js b/extensions/cornerstone/src/initCornerstoneTools.js index 2d305af8a..5df8f8983 100644 --- a/extensions/cornerstone/src/initCornerstoneTools.js +++ b/extensions/cornerstone/src/initCornerstoneTools.js @@ -9,6 +9,7 @@ import { LengthTool, RectangleROITool, EllipticalROITool, + CircleROITool, BidirectionalTool, ArrowAnnotateTool, DragProbeTool, @@ -41,6 +42,7 @@ export default function initCornerstoneTools(configuration = {}) { addTool(LengthTool); addTool(RectangleROITool); addTool(EllipticalROITool); + addTool(CircleROITool); addTool(BidirectionalTool); addTool(ArrowAnnotateTool); addTool(DragProbeTool); @@ -83,6 +85,7 @@ const toolNames = { Probe: ProbeTool.toolName, RectangleROI: RectangleROITool.toolName, EllipticalROI: EllipticalROITool.toolName, + CircleROI: CircleROITool.toolName, Bidirectional: BidirectionalTool.toolName, Angle: AngleTool.toolName, CobbAngle: CobbAngleTool.toolName, diff --git a/extensions/cornerstone/src/initMeasurementService.js b/extensions/cornerstone/src/initMeasurementService.js index 36b7229d2..c11a53111 100644 --- a/extensions/cornerstone/src/initMeasurementService.js +++ b/extensions/cornerstone/src/initMeasurementService.js @@ -24,6 +24,7 @@ const initMeasurementService = ( Length, Bidirectional, EllipticalROI, + CircleROI, ArrowAnnotate, Angle, CobbAngle, @@ -78,6 +79,14 @@ const initMeasurementService = ( EllipticalROI.toMeasurement ); + measurementService.addMapping( + csTools3DVer1MeasurementSource, + 'CircleROI', + CircleROI.matchingCriteria, + CircleROI.toAnnotation, + CircleROI.toMeasurement + ); + measurementService.addMapping( csTools3DVer1MeasurementSource, 'ArrowAnnotate', diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/ArrowAnnotate.js b/extensions/cornerstone/src/utils/measurementServiceMappings/ArrowAnnotate.ts similarity index 100% rename from extensions/cornerstone/src/utils/measurementServiceMappings/ArrowAnnotate.js rename to extensions/cornerstone/src/utils/measurementServiceMappings/ArrowAnnotate.ts diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/Bidirectional.js b/extensions/cornerstone/src/utils/measurementServiceMappings/Bidirectional.ts similarity index 100% rename from extensions/cornerstone/src/utils/measurementServiceMappings/Bidirectional.js rename to extensions/cornerstone/src/utils/measurementServiceMappings/Bidirectional.ts diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/CircleROI.ts b/extensions/cornerstone/src/utils/measurementServiceMappings/CircleROI.ts new file mode 100644 index 000000000..c55d7da4b --- /dev/null +++ b/extensions/cornerstone/src/utils/measurementServiceMappings/CircleROI.ts @@ -0,0 +1,228 @@ +import SUPPORTED_TOOLS from './constants/supportedTools'; +import getSOPInstanceAttributes from './utils/getSOPInstanceAttributes'; +import getModalityUnit from './utils/getModalityUnit'; +import { utils } from '@ohif/core'; + +const CircleROI = { + toAnnotation: measurement => {}, + toMeasurement: ( + csToolsEventDetail, + DisplaySetService, + CornerstoneViewportService, + getValueTypeFromToolType + ) => { + const { annotation, viewportId } = csToolsEventDetail; + const { metadata, data, annotationUID } = annotation; + + if (!metadata || !data) { + console.warn('Length tool: Missing metadata or data'); + return null; + } + + const { toolName, referencedImageId, FrameOfReferenceUID } = metadata; + const validToolType = SUPPORTED_TOOLS.includes(toolName); + + if (!validToolType) { + throw new Error('Tool not supported'); + } + + const { + SOPInstanceUID, + SeriesInstanceUID, + StudyInstanceUID, + } = getSOPInstanceAttributes( + referencedImageId, + CornerstoneViewportService, + viewportId + ); + + let displaySet; + + if (SOPInstanceUID) { + displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID( + SOPInstanceUID, + SeriesInstanceUID + ); + } else { + displaySet = DisplaySetService.getDisplaySetsForSeries(SeriesInstanceUID); + } + + const { points } = data.handles; + + const mappedAnnotations = getMappedAnnotations( + annotation, + DisplaySetService + ); + + const displayText = getDisplayText(mappedAnnotations, displaySet); + const getReport = () => + _getReport(mappedAnnotations, points, FrameOfReferenceUID); + + return { + uid: annotationUID, + SOPInstanceUID, + FrameOfReferenceUID, + points, + metadata, + referenceSeriesUID: SeriesInstanceUID, + referenceStudyUID: StudyInstanceUID, + frameNumber: mappedAnnotations[0]?.frameNumber || 1, + toolName: metadata.toolName, + displaySetInstanceUID: displaySet.displaySetInstanceUID, + label: data.label, + displayText: displayText, + data: data.cachedStats, + type: getValueTypeFromToolType(toolName), + getReport, + }; + }, +}; + +function getMappedAnnotations(annotation, DisplaySetService) { + const { metadata, data } = annotation; + const { cachedStats } = data; + const { referencedImageId } = metadata; + const targets = Object.keys(cachedStats); + + if (!targets.length) { + return []; + } + + const annotations = []; + Object.keys(cachedStats).forEach(targetId => { + const targetStats = cachedStats[targetId]; + + if (!referencedImageId) { + // Todo: Non-acquisition plane measurement mapping not supported yet + throw new Error( + 'Non-acquisition plane measurement mapping not supported' + ); + } + + const { + SOPInstanceUID, + SeriesInstanceUID, + frameNumber, + } = getSOPInstanceAttributes(referencedImageId); + + const displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID( + SOPInstanceUID, + SeriesInstanceUID, + frameNumber + ); + + const { SeriesNumber } = displaySet; + const { mean, stdDev, max, area, Modality } = targetStats; + const unit = getModalityUnit(Modality); + + annotations.push({ + SeriesInstanceUID, + SOPInstanceUID, + SeriesNumber, + frameNumber, + Modality, + unit, + mean, + stdDev, + max, + area, + }); + }); + + return annotations; +} + +/* +This function is used to convert the measurement data to a format that is +suitable for the report generation (e.g. for the csv report). The report +returns a list of columns and corresponding values. +*/ +function _getReport(mappedAnnotations, points, FrameOfReferenceUID) { + const columns = []; + const values = []; + + // Add Type + columns.push('AnnotationType'); + values.push('Cornerstone:CircleROI'); + + mappedAnnotations.forEach(annotation => { + const { mean, stdDev, max, area, unit } = annotation; + + if (!mean || !unit || !max || !area) { + return; + } + + columns.push( + `max (${unit})`, + `mean (${unit})`, + `std (${unit})`, + `area (mm2)` + ); + values.push(max, mean, stdDev, area); + }); + + if (FrameOfReferenceUID) { + columns.push('FrameOfReferenceUID'); + values.push(FrameOfReferenceUID); + } + + if (points) { + columns.push('points'); + // points has the form of [[x1, y1, z1], [x2, y2, z2], ...] + // convert it to string of [[x1 y1 z1];[x2 y2 z2];...] + // so that it can be used in the csv report + values.push(points.map(p => p.join(' ')).join(';')); + } + + return { + columns, + values, + }; +} + +function getDisplayText(mappedAnnotations, displaySet) { + if (!mappedAnnotations || !mappedAnnotations.length) { + return ''; + } + + const displayText = []; + + // Area is the same for all series + const { area, SOPInstanceUID, frameNumber } = mappedAnnotations[0]; + + const instance = displaySet.images.find( + image => image.SOPInstanceUID === SOPInstanceUID + ); + + let InstanceNumber; + if (instance) { + InstanceNumber = instance.InstanceNumber; + } + + const instanceText = InstanceNumber ? ` I: ${InstanceNumber}` : ''; + const frameText = displaySet.isMultiFrame ? ` F: ${frameNumber}` : ''; + + // Area sometimes becomes undefined if `preventHandleOutsideImage` is off. + const roundedArea = utils.roundNumber(area || 0, 2); + displayText.push(`${roundedArea} mm2`); + + // Todo: we need a better UI for displaying all these information + mappedAnnotations.forEach(mappedAnnotation => { + const { unit, max, SeriesNumber } = mappedAnnotation; + + let maxStr = ''; + if (max) { + const roundedMax = utils.roundNumber(max, 2); + maxStr = `Max: ${roundedMax} ${unit} `; + } + + const str = `${maxStr}(S:${SeriesNumber}${instanceText}${frameText})`; + if (!displayText.includes(str)) { + displayText.push(str); + } + }); + + return displayText; +} + +export default CircleROI; diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/EllipticalROI.js b/extensions/cornerstone/src/utils/measurementServiceMappings/EllipticalROI.ts similarity index 100% rename from extensions/cornerstone/src/utils/measurementServiceMappings/EllipticalROI.js rename to extensions/cornerstone/src/utils/measurementServiceMappings/EllipticalROI.ts diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/Length.js b/extensions/cornerstone/src/utils/measurementServiceMappings/Length.ts similarity index 90% rename from extensions/cornerstone/src/utils/measurementServiceMappings/Length.js rename to extensions/cornerstone/src/utils/measurementServiceMappings/Length.ts index 206208257..8dad5a1c1 100644 --- a/extensions/cornerstone/src/utils/measurementServiceMappings/Length.js +++ b/extensions/cornerstone/src/utils/measurementServiceMappings/Length.ts @@ -1,6 +1,6 @@ import SUPPORTED_TOOLS from './constants/supportedTools'; import getSOPInstanceAttributes from './utils/getSOPInstanceAttributes'; -import { displaySetService, utils } from '@ohif/core'; +import { utils } from '@ohif/core'; const Length = { toAnnotation: measurement => {}, @@ -32,15 +32,12 @@ const Length = { throw new Error('Tool not supported'); } - const { - SOPInstanceUID, - SeriesInstanceUID, - StudyInstanceUID, - } = getSOPInstanceAttributes( - referencedImageId, - cornerstoneViewportService, - viewportId - ); + const { SOPInstanceUID, SeriesInstanceUID, StudyInstanceUID } = + getSOPInstanceAttributes( + referencedImageId, + cornerstoneViewportService, + viewportId + ); let displaySet; @@ -104,11 +101,8 @@ function getMappedAnnotations(annotation, displaySetService) { ); } - const { - SOPInstanceUID, - SeriesInstanceUID, - frameNumber, - } = getSOPInstanceAttributes(referencedImageId); + const { SOPInstanceUID, SeriesInstanceUID, frameNumber } = + getSOPInstanceAttributes(referencedImageId); const displaySet = displaySetService.getDisplaySetForSOPInstanceUID( SOPInstanceUID, @@ -179,12 +173,8 @@ function getDisplayText(mappedAnnotations, displaySet) { const displayText = []; // Area is the same for all series - const { - length, - SeriesNumber, - SOPInstanceUID, - frameNumber, - } = mappedAnnotations[0]; + const { length, SeriesNumber, SOPInstanceUID, frameNumber } = + mappedAnnotations[0]; const instance = displaySet.images.find( image => image.SOPInstanceUID === SOPInstanceUID diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/RectangleROI.ts b/extensions/cornerstone/src/utils/measurementServiceMappings/RectangleROI.ts index 7560dc137..01f1178b9 100644 --- a/extensions/cornerstone/src/utils/measurementServiceMappings/RectangleROI.ts +++ b/extensions/cornerstone/src/utils/measurementServiceMappings/RectangleROI.ts @@ -4,7 +4,7 @@ import getModalityUnit from './utils/getModalityUnit'; import { utils } from '@ohif/core'; const RectangleROI = { - toAnnotation: measurement => { }, + toAnnotation: measurement => {}, toMeasurement: ( csToolsEventDetail, DisplaySetService, @@ -26,15 +26,12 @@ const RectangleROI = { throw new Error('Tool not supported'); } - const { - SOPInstanceUID, - SeriesInstanceUID, - StudyInstanceUID, - } = getSOPInstanceAttributes( - referencedImageId, - CornerstoneViewportService, - viewportId - ); + const { SOPInstanceUID, SeriesInstanceUID, StudyInstanceUID } = + getSOPInstanceAttributes( + referencedImageId, + CornerstoneViewportService, + viewportId + ); let displaySet; @@ -99,11 +96,8 @@ function getMappedAnnotations(annotation, DisplaySetService) { ); } - const { - SOPInstanceUID, - SeriesInstanceUID, - frameNumber, - } = getSOPInstanceAttributes(referencedImageId); + const { SOPInstanceUID, SeriesInstanceUID, frameNumber } = + getSOPInstanceAttributes(referencedImageId); const displaySet = DisplaySetService.getDisplaySetForSOPInstanceUID( SOPInstanceUID, @@ -143,7 +137,7 @@ function _getReport(mappedAnnotations, points, FrameOfReferenceUID) { // Add Type columns.push('AnnotationType'); - values.push('Cornerstone:EllipticalROI'); + values.push('Cornerstone:RectangleROI'); mappedAnnotations.forEach(annotation => { const { mean, stdDev, max, area, unit } = annotation; diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/constants/supportedTools.js b/extensions/cornerstone/src/utils/measurementServiceMappings/constants/supportedTools.js index 00be9ae14..e1e8a1755 100644 --- a/extensions/cornerstone/src/utils/measurementServiceMappings/constants/supportedTools.js +++ b/extensions/cornerstone/src/utils/measurementServiceMappings/constants/supportedTools.js @@ -1,6 +1,7 @@ export default [ 'Length', 'EllipticalROI', + 'CircleROI', 'Bidirectional', 'ArrowAnnotate', 'Angle', diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.ts b/extensions/cornerstone/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.ts index 4d5c77f17..2a4562e7d 100644 --- a/extensions/cornerstone/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.ts +++ b/extensions/cornerstone/src/utils/measurementServiceMappings/measurementServiceMappingsFactory.ts @@ -2,6 +2,7 @@ import { MeasurementService } from '@ohif/core'; import Length from './Length'; import Bidirectional from './Bidirectional'; import EllipticalROI from './EllipticalROI'; +import CircleROI from './CircleROI'; import ArrowAnnotate from './ArrowAnnotate'; import CobbAngle from './CobbAngle'; import Angle from './Angle'; @@ -25,6 +26,7 @@ const measurementServiceMappingsFactory = ( const { POLYLINE, ELLIPSE, + CIRCLE, RECTANGLE, BIDIRECTIONAL, POINT, @@ -37,6 +39,7 @@ const measurementServiceMappingsFactory = ( const TOOL_TYPE_TO_VALUE_TYPE = { Length: POLYLINE, EllipticalROI: ELLIPSE, + CircleROI: CIRCLE, RectangleROI: RECTANGLE, PlanarFreehandROI: POLYLINE, Bidirectional: BIDIRECTIONAL, @@ -104,6 +107,22 @@ const measurementServiceMappingsFactory = ( ], }, + CircleROI: { + toAnnotation: CircleROI.toAnnotation, + toMeasurement: csToolsAnnotation => + CircleROI.toMeasurement( + csToolsAnnotation, + displaySetService, + cornerstoneViewportService, + _getValueTypeFromToolType + ), + matchingCriteria: [ + { + valueType: MeasurementService.VALUE_TYPES.CIRCLE, + }, + ], + }, + RectangleROI: { toAnnotation: RectangleROI.toAnnotation, toMeasurement: csToolsAnnotation => diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/utils/getSOPInstanceAttributes.js b/extensions/cornerstone/src/utils/measurementServiceMappings/utils/getSOPInstanceAttributes.js index b93226bb1..c0707dd4f 100644 --- a/extensions/cornerstone/src/utils/measurementServiceMappings/utils/getSOPInstanceAttributes.js +++ b/extensions/cornerstone/src/utils/measurementServiceMappings/utils/getSOPInstanceAttributes.js @@ -13,8 +13,8 @@ import * as cornerstone from '@cornerstonejs/core'; */ export default function getSOPInstanceAttributes( imageId, - cornerstoneViewportService, - viewportId + cornerstoneViewportService = undefined, + viewportId = undefined ) { if (imageId) { return _getUIDFromImageID(imageId); diff --git a/extensions/default/package.json b/extensions/default/package.json index 0ca309f62..81ca66393 100644 --- a/extensions/default/package.json +++ b/extensions/default/package.json @@ -32,7 +32,7 @@ "peerDependencies": { "@ohif/core": "^3.0.0", "@ohif/i18n": "^1.0.0", - "dcmjs": "^0.29.4", + "dcmjs": "^0.29.5", "dicomweb-client": "^0.8.4", "prop-types": "^15.6.2", "react": "^17.0.2", diff --git a/extensions/dicom-pdf/package.json b/extensions/dicom-pdf/package.json index 85684879c..1de3bce06 100644 --- a/extensions/dicom-pdf/package.json +++ b/extensions/dicom-pdf/package.json @@ -30,7 +30,7 @@ "peerDependencies": { "@ohif/core": "^3.0.0", "@ohif/ui": "^2.0.0", - "dcmjs": "^0.29.4", + "dcmjs": "^0.29.5", "dicom-parser": "^1.8.9", "hammerjs": "^2.0.8", "prop-types": "^15.6.2", diff --git a/extensions/dicom-video/package.json b/extensions/dicom-video/package.json index 83f4e060b..6447fa568 100644 --- a/extensions/dicom-video/package.json +++ b/extensions/dicom-video/package.json @@ -30,7 +30,7 @@ "peerDependencies": { "@ohif/core": "^3.0.0", "@ohif/ui": "^2.0.0", - "dcmjs": "^0.29.4", + "dcmjs": "^0.29.5", "dicom-parser": "^1.8.9", "hammerjs": "^2.0.8", "prop-types": "^15.6.2", diff --git a/extensions/measurement-tracking/package.json b/extensions/measurement-tracking/package.json index 332d84253..59ab9e3b9 100644 --- a/extensions/measurement-tracking/package.json +++ b/extensions/measurement-tracking/package.json @@ -35,7 +35,7 @@ "@cornerstonejs/core": "^0.40.0", "@cornerstonejs/tools": "^0.60.1", "@ohif/extension-cornerstone-dicom-sr": "^3.0.0", - "dcmjs": "^0.29.4", + "dcmjs": "^0.29.5", "lodash.debounce": "^4.17.21", "prop-types": "^15.6.2", "react": "^17.0.2", diff --git a/extensions/tmtv/package.json b/extensions/tmtv/package.json index 9210d7cfa..89d25ba3b 100644 --- a/extensions/tmtv/package.json +++ b/extensions/tmtv/package.json @@ -30,7 +30,7 @@ "peerDependencies": { "@ohif/core": "^3.0.0", "@ohif/ui": "^2.0.0", - "dcmjs": "^0.29.4", + "dcmjs": "^0.29.5", "dicom-parser": "^1.8.9", "hammerjs": "^2.0.8", "prop-types": "^15.6.2", diff --git a/modes/basic-dev-mode/src/index.js b/modes/basic-dev-mode/src/index.js index d74ee60a4..229feb643 100644 --- a/modes/basic-dev-mode/src/index.js +++ b/modes/basic-dev-mode/src/index.js @@ -81,6 +81,7 @@ function modeFactory({ modeConfiguration }) { { toolName: toolNames.Bidirectional }, { toolName: toolNames.Probe }, { toolName: toolNames.EllipticalROI }, + { toolName: toolNames.CircleROI }, { toolName: toolNames.RectangleROI }, { toolName: toolNames.StackScroll }, { toolName: toolNames.CalibrationLine }, @@ -134,11 +135,8 @@ function modeFactory({ modeConfiguration }) { ]); }, onModeExit: ({ servicesManager }) => { - const { - toolGroupService, - measurementService, - toolbarService, - } = servicesManager.services; + const { toolGroupService, measurementService, toolbarService } = + servicesManager.services; toolGroupService.destroy(); }, diff --git a/modes/basic-dev-mode/src/toolbarButtons.js b/modes/basic-dev-mode/src/toolbarButtons.js index 4a08edbf0..995e4dea6 100644 --- a/modes/basic-dev-mode/src/toolbarButtons.js +++ b/modes/basic-dev-mode/src/toolbarButtons.js @@ -130,6 +130,21 @@ const toolbarButtons = [ ], 'Ellipse Tool' ), + _createToolButton( + 'CircleROI', + 'tool-circle', + 'Circle', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'CircleROI', + }, + context: 'CORNERSTONE', + }, + ], + 'Circle Tool' + ), ], }, }, diff --git a/modes/basic-test-mode/src/initToolGroups.js b/modes/basic-test-mode/src/initToolGroups.js index 105b1a2f8..ccc5c1a6d 100644 --- a/modes/basic-test-mode/src/initToolGroups.js +++ b/modes/basic-test-mode/src/initToolGroups.js @@ -32,6 +32,7 @@ function initDefaultToolGroup( { toolName: toolNames.Bidirectional }, { toolName: toolNames.DragProbe }, { toolName: toolNames.EllipticalROI }, + { toolName: toolNames.CircleROI }, { toolName: toolNames.RectangleROI }, { toolName: toolNames.StackScroll }, { toolName: toolNames.Angle }, @@ -110,6 +111,7 @@ function initSRToolGroup(extensionManager, toolGroupService, commandsManager) { { toolName: SRToolNames.SRArrowAnnotate }, { toolName: SRToolNames.SRBidirectional }, { toolName: SRToolNames.SREllipticalROI }, + { toolName: SRToolNames.SRCircleROI }, ], enabled: [ { @@ -170,6 +172,7 @@ function initMPRToolGroup(extensionManager, toolGroupService, commandsManager) { { toolName: toolNames.Bidirectional }, { toolName: toolNames.DragProbe }, { toolName: toolNames.EllipticalROI }, + { toolName: toolNames.CircleROI }, { toolName: toolNames.RectangleROI }, { toolName: toolNames.StackScroll }, { toolName: toolNames.Angle }, diff --git a/modes/basic-test-mode/src/toolbarButtons.js b/modes/basic-test-mode/src/toolbarButtons.js index 9a04581c5..2d0492f6d 100644 --- a/modes/basic-test-mode/src/toolbarButtons.js +++ b/modes/basic-test-mode/src/toolbarButtons.js @@ -200,6 +200,29 @@ const toolbarButtons = [ ], 'Ellipse Tool' ), + _createToolButton( + 'CircleROI', + 'tool-circle', + 'Circle', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'CircleROI', + }, + context: 'CORNERSTONE', + }, + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'SRCircleROI', + toolGroupId: 'SRToolGroup', + }, + context: 'CORNERSTONE', + }, + ], + 'Circle Tool' + ), ], }, }, diff --git a/modes/longitudinal/src/initToolGroups.js b/modes/longitudinal/src/initToolGroups.js index 6bbe668d2..b8e88db90 100644 --- a/modes/longitudinal/src/initToolGroups.js +++ b/modes/longitudinal/src/initToolGroups.js @@ -32,6 +32,7 @@ function initDefaultToolGroup( { toolName: toolNames.Bidirectional }, { toolName: toolNames.DragProbe }, { toolName: toolNames.EllipticalROI }, + { toolName: toolNames.CircleROI }, { toolName: toolNames.RectangleROI }, { toolName: toolNames.StackScroll }, { toolName: toolNames.Angle }, @@ -113,6 +114,7 @@ function initSRToolGroup(extensionManager, toolGroupService, commandsManager) { { toolName: SRToolNames.SRArrowAnnotate }, { toolName: SRToolNames.SRBidirectional }, { toolName: SRToolNames.SREllipticalROI }, + { toolName: SRToolNames.SRCircleROI }, ], enabled: [ { @@ -173,6 +175,7 @@ function initMPRToolGroup(extensionManager, toolGroupService, commandsManager) { { toolName: toolNames.Bidirectional }, { toolName: toolNames.DragProbe }, { toolName: toolNames.EllipticalROI }, + { toolName: toolNames.CircleROI }, { toolName: toolNames.RectangleROI }, { toolName: toolNames.StackScroll }, { toolName: toolNames.Angle }, diff --git a/modes/longitudinal/src/toolbarButtons.js b/modes/longitudinal/src/toolbarButtons.js index a2b72cbf1..92de37e89 100644 --- a/modes/longitudinal/src/toolbarButtons.js +++ b/modes/longitudinal/src/toolbarButtons.js @@ -208,6 +208,29 @@ const toolbarButtons = [ ], 'Ellipse Tool' ), + _createToolButton( + 'CircleROI', + 'tool-circle', + 'Circle', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'CircleROI', + }, + context: 'CORNERSTONE', + }, + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'SRCircleROI', + toolGroupId: 'SRToolGroup', + }, + context: 'CORNERSTONE', + }, + ], + 'Circle Tool' + ), ], }, }, diff --git a/modes/tmtv/src/toolbarButtons.js b/modes/tmtv/src/toolbarButtons.js index 8fd347737..f6f707221 100644 --- a/modes/tmtv/src/toolbarButtons.js +++ b/modes/tmtv/src/toolbarButtons.js @@ -173,6 +173,20 @@ const toolbarButtons = [ ], 'Ellipse Tool' ), + _createToolButton( + 'CircleROI', + 'tool-circle', + 'Circle', + [ + ..._createCommands('setToolActive', 'CircleROI', [ + toolGroupIds.CT, + toolGroupIds.PT, + toolGroupIds.Fusion, + // toolGroupIds.MPR, + ]), + ], + 'Circle Tool' + ), ], }, }, @@ -299,8 +313,7 @@ const toolbarButtons = [ commandName: 'displayNotification', commandOptions: { title: 'RectangleROI Threshold Tip', - text: - 'RectangleROI Threshold tool should be used on PT Axial Viewport', + text: 'RectangleROI Threshold tool should be used on PT Axial Viewport', type: 'info', }, }, diff --git a/platform/core/package.json b/platform/core/package.json index 42c973065..cb97a9eab 100644 --- a/platform/core/package.json +++ b/platform/core/package.json @@ -37,7 +37,7 @@ }, "dependencies": { "@babel/runtime": "^7.20.13", - "dcmjs": "^0.29.4", + "dcmjs": "^0.29.5", "dicomweb-client": "^0.8.4", "isomorphic-base64": "^1.0.2", "lodash.merge": "^4.6.1", diff --git a/platform/core/src/utils/roundNumber.js b/platform/core/src/utils/roundNumber.js index b62e5df42..a441225da 100644 --- a/platform/core/src/utils/roundNumber.js +++ b/platform/core/src/utils/roundNumber.js @@ -1,5 +1,9 @@ +/** + * @param {string | number} value + * @param {number} decimals + */ function _round(value, decimals) { - return Number(value.toFixed(decimals)); + return Number(value).toFixed(decimals); } export default _round; diff --git a/platform/docs/versioned_docs/version-3.0/platform/extensions/modules/toolbar.md b/platform/docs/versioned_docs/version-3.0/platform/extensions/modules/toolbar.md index f340e0c4e..98e0d91a7 100644 --- a/platform/docs/versioned_docs/version-3.0/platform/extensions/modules/toolbar.md +++ b/platform/docs/versioned_docs/version-3.0/platform/extensions/modules/toolbar.md @@ -184,6 +184,16 @@ to create `MeasurementTools` nested button toolName: 'EllipticalRoi', } }, + // Circle tool + { + id: 'CircleROI', + icon: 'tool-circle', + label: 'Circle', + type: 'tool', + commandOptions: { + toolName: 'CircleROI', + } + }, ], }, } diff --git a/platform/docs/versioned_docs/version-3.0/platform/services/data/ToolbarService.md b/platform/docs/versioned_docs/version-3.0/platform/services/data/ToolbarService.md index b080c6ef4..92ab50048 100644 --- a/platform/docs/versioned_docs/version-3.0/platform/services/data/ToolbarService.md +++ b/platform/docs/versioned_docs/version-3.0/platform/services/data/ToolbarService.md @@ -210,6 +210,16 @@ to create `MeasurementTools` nested button toolName: 'EllipticalRoi', } }, + // Circle tool + { + id: 'CircleROI', + icon: 'tool-circle', + label: 'Circle', + type: 'tool', + commandOptions: { + toolName: 'CircleROI', + } + }, ], }, } diff --git a/platform/ui/src/assets/icons/tool-circle.svg b/platform/ui/src/assets/icons/tool-circle.svg new file mode 100644 index 000000000..e94375564 --- /dev/null +++ b/platform/ui/src/assets/icons/tool-circle.svg @@ -0,0 +1,3 @@ + + + diff --git a/platform/ui/src/components/Icon/getIcon.js b/platform/ui/src/components/Icon/getIcon.js index e6c3b986a..b8df5463d 100644 --- a/platform/ui/src/components/Icon/getIcon.js +++ b/platform/ui/src/components/Icon/getIcon.js @@ -81,6 +81,7 @@ import toolWindow from './../../assets/icons/tool-window-level.svg'; import toolAnnotate from './../../assets/icons/tool-annotate.svg'; import toolBidirectional from './../../assets/icons/tool-bidirectional.svg'; import toolElipse from './../../assets/icons/tool-elipse.svg'; +import toolCircle from './../../assets/icons/tool-circle.svg'; import toolLength from './../../assets/icons/tool-length.svg'; import toolStackScroll from './../../assets/icons/tool-stack-scroll.svg'; import toolMagnify from './../../assets/icons/tool-magnify.svg'; @@ -199,6 +200,7 @@ const ICONS = { 'tool-annotate': toolAnnotate, 'tool-bidirectional': toolBidirectional, 'tool-elipse': toolElipse, + 'tool-circle': toolCircle, 'tool-length': toolLength, 'tool-stack-scroll': toolStackScroll, 'tool-magnify': toolMagnify, diff --git a/platform/viewer/package.json b/platform/viewer/package.json index 60bbf2f42..2c1c7325b 100644 --- a/platform/viewer/package.json +++ b/platform/viewer/package.json @@ -66,7 +66,7 @@ "core-js": "^3.16.1", "cornerstone-math": "^0.1.9", "cornerstone-wado-image-loader": "^4.13.0", - "dcmjs": "^0.29.4", + "dcmjs": "^0.29.5", "detect-gpu": "^4.0.16", "dicom-parser": "^1.8.9", "dotenv-webpack": "^1.7.0", diff --git a/yarn.lock b/yarn.lock index e5d1f8dde..5611ea7a2 100644 --- a/yarn.lock +++ b/yarn.lock @@ -9247,21 +9247,9 @@ dayjs@^1.10.4: resolved "https://registry.npmjs.org/dayjs/-/dayjs-1.11.7.tgz#4b296922642f70999544d1144a2c25730fce63e2" integrity sha512-+Yw9U6YO5TQohxLcIkrXBeY73WP3ejHWVvx8XCk3gxvQDCTEmS48ZrSZCKciI7Bhl/uCMyxYtE9UqRILmFphkQ== -dcmjs@^0.29.4: - version "0.29.4" - resolved "https://registry.npmjs.org/dcmjs/-/dcmjs-0.29.4.tgz#3fb13945611979f756bc91b3f199fd87b4eabdb4" - integrity sha512-PzD6C4oB7v/AVTIPbkS6D6hjgVcSW7+T+DsxFpkD1xcEgU4qjGM16WGEHH3ZAPDBF0Xgm2d9FXUu/lXZIyfmow== - dependencies: - "@babel/runtime-corejs2" "^7.17.8" - gl-matrix "^3.1.0" - lodash.clonedeep "^4.5.0" - loglevelnext "^3.0.1" - ndarray "^1.0.19" - pako "^2.0.4" - dcmjs@^0.29.5: version "0.29.5" - resolved "https://registry.npmjs.org/dcmjs/-/dcmjs-0.29.5.tgz#3e2311fc47aafc70f21e236ad89e2ff9ba6589fd" + resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.29.5.tgz#3e2311fc47aafc70f21e236ad89e2ff9ba6589fd" integrity sha512-CcLo3pwitf9JhhvW3/icCraxUhaIKJRyOys9XJlBBDn5TQskyJzxgveLKejcryHn4DooqlJPeMuM4ixdPFEERQ== dependencies: "@babel/runtime-corejs2" "^7.17.8" From 6cf271d006713d631cea9a061e472b2930ce98ae Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Tue, 18 Apr 2023 11:17:50 -0400 Subject: [PATCH 10/54] fix: Service consistency typing (#3309) * Use more consistent type/structure for services * Fix restoring SR so the tests described work * One more typed service * Added types for the Cornerstone library * Couple more type fixes --- .../cornerstone-dicom-seg/src/index.tsx | 11 -- extensions/cornerstone-dicom-sr/package.json | 4 +- .../viewports/OHIFCornerstoneSRViewport.tsx | 15 ++- extensions/cornerstone/package.json | 5 + .../src/Viewport/OHIFCornerstoneViewport.tsx | 13 +-- extensions/cornerstone/src/index.tsx | 24 ++--- .../CornerstoneCacheService.ts | 21 ++-- .../SegmentationService.ts | 21 ++-- .../src/services/SegmentationService/index.js | 10 +- .../SyncGroupService/SyncGroupService.ts | 18 +++- .../src/services/SyncGroupService/index.js | 10 +- .../ToolGroupService/ToolGroupService.ts | 18 ++-- .../CornerstoneViewportService.ts | 29 ++--- .../src/types/CornerstoneServices.ts | 16 +++ extensions/cornerstone/src/types/index.ts | 4 +- .../src/CustomizeableContextMenu/index.ts | 2 +- platform/core/package.json | 1 + .../core/src/extensions/ExtensionManager.ts | 5 +- .../core/src/services/UIModalService/index.js | 91 ---------------- .../core/src/services/UIModalService/index.ts | 87 +++++++++++++++ .../services/UINotificationService/index.js | 101 ------------------ .../services/UINotificationService/index.ts | 94 ++++++++++++++++ platform/core/src/types/Services.ts | 6 +- platform/ui/src/types/index.ts | 2 +- 24 files changed, 309 insertions(+), 299 deletions(-) create mode 100644 extensions/cornerstone/src/types/CornerstoneServices.ts delete mode 100644 platform/core/src/services/UIModalService/index.js create mode 100644 platform/core/src/services/UIModalService/index.ts delete mode 100644 platform/core/src/services/UINotificationService/index.js create mode 100644 platform/core/src/services/UINotificationService/index.ts diff --git a/extensions/cornerstone-dicom-seg/src/index.tsx b/extensions/cornerstone-dicom-seg/src/index.tsx index e4ea1944c..fde3d95a9 100644 --- a/extensions/cornerstone-dicom-seg/src/index.tsx +++ b/extensions/cornerstone-dicom-seg/src/index.tsx @@ -30,17 +30,6 @@ const extension = { */ id, - /** - * Perform any pre-registration tasks here. This is called before the extension - * is registered. Usually we run tasks such as: configuring the libraries - * (e.g. cornerstone, cornerstoneTools, ...) or registering any services that - * this extension is providing. - */ - preRegistration: ({ - servicesManager, - commandsManager, - configuration = {}, - }) => {}, /** * PanelModule should provide a list of panels that will be available in OHIF * for Modes to consume and render. Each panel is defined by a {name, diff --git a/extensions/cornerstone-dicom-sr/package.json b/extensions/cornerstone-dicom-sr/package.json index 76e8fe82b..a566c0c0d 100644 --- a/extensions/cornerstone-dicom-sr/package.json +++ b/extensions/cornerstone-dicom-sr/package.json @@ -32,8 +32,8 @@ "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests" }, "peerDependencies": { - "@ohif/core": "^3.0.0", - "@ohif/extension-cornerstone": "^3.0.0", + "@ohif/core": ">=3.0.0", + "@ohif/extension-cornerstone": ">=3.0.0", "@ohif/extension-measurement-tracking": "^3.0.0", "@ohif/ui": "^2.0.0", "dcmjs": "^0.29.5", diff --git a/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx b/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx index c16b6a334..c3db19b8c 100644 --- a/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx +++ b/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx @@ -2,6 +2,8 @@ import PropTypes from 'prop-types'; import React, { useCallback, useContext, useEffect, useState } from 'react'; import { useTranslation } from 'react-i18next'; import OHIF, { utils, ServicesManager, ExtensionManager } from '@ohif/core'; +import { CornerstoneServices } from '@ohif/extension-cornerstone/types'; + import { setTrackingUniqueIdentifiersForElement } from '../tools/modules/dicomSRModule'; import { @@ -37,7 +39,7 @@ function OHIFCornerstoneSRViewport(props) { displaySetService, cornerstoneViewportService, measurementService, - } = servicesManager.services; + } = servicesManager.services as CornerstoneServices; // SR viewport will always have a single display set if (displaySets.length > 1) { @@ -91,10 +93,12 @@ function OHIFCornerstoneSRViewport(props) { SeriesInstanceUIDs[0] ); if (displaySets.length) { - viewportGridService.setDisplaySetsForViewport({ - viewportIndex: activeViewportIndex, - displaySetInstanceUIDs: [displaySets[0].displaySetInstanceUID], - }); + viewportGridService.setDisplaySetsForViewports([ + { + viewportIndex: activeViewportIndex, + displaySetInstanceUIDs: [displaySets[0].displaySetInstanceUID], + }, + ]); } }; } @@ -422,6 +426,7 @@ OHIFCornerstoneSRViewport.propTypes = { children: PropTypes.node, customProps: PropTypes.object, viewportOptions: PropTypes.object, + viewportLabel: PropTypes.string, servicesManager: PropTypes.instanceOf(ServicesManager).isRequired, extensionManager: PropTypes.instanceOf(ExtensionManager).isRequired, }; diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json index cae1befd0..55a5b76d9 100644 --- a/extensions/cornerstone/package.json +++ b/extensions/cornerstone/package.json @@ -7,6 +7,11 @@ "repository": "OHIF/Viewers", "main": "dist/index.umd.js", "module": "src/index.tsx", + "types": "src/types/index.ts", + "exports": { + ".": "./src/index.tsx", + "./types": "./src/types/index.ts" + }, "engines": { "node": ">=10", "npm": ">=6", diff --git a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx index fb51ccdd6..0a9d8ac89 100644 --- a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx +++ b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx @@ -10,17 +10,18 @@ import { utilities as csUtils, CONSTANTS, } from '@cornerstonejs/core'; +import { CinePlayer, useCine, useViewportGrid } from '@ohif/ui'; +import { + IStackViewport, + IVolumeViewport, +} from '@cornerstonejs/core/dist/esm/types'; import { setEnabledElement } from '../state'; import './OHIFCornerstoneViewport.css'; import CornerstoneOverlays from './Overlays/CornerstoneOverlays'; -import { - IStackViewport, - IVolumeViewport, -} from '@cornerstonejs/core/dist/esm/types'; import getSOPInstanceAttributes from '../utils/measurementServiceMappings/utils/getSOPInstanceAttributes'; -import { CinePlayer, useCine, useViewportGrid } from '@ohif/ui'; +import CornerstoneServices from '../types/CornerstoneServices'; const STACK = 'stack'; @@ -129,7 +130,7 @@ const OHIFCornerstoneViewport = React.memo(props => { cornerstoneCacheService, viewportGridService, stateSyncService, - } = servicesManager.services; + } = servicesManager.services as CornerstoneServices; const cineHandler = () => { if (!cines || !cines[viewportIndex] || !enabledVPElement) { diff --git a/extensions/cornerstone/src/index.tsx b/extensions/cornerstone/src/index.tsx index f1ec22f16..165d70cd9 100644 --- a/extensions/cornerstone/src/index.tsx +++ b/extensions/cornerstone/src/index.tsx @@ -7,7 +7,7 @@ import { imageRetrievalPoolManager, } from '@cornerstonejs/core'; import { Enums as cs3DToolsEnums } from '@cornerstonejs/tools'; -import { Types } from '@ohif/core'; +import { ServicesManager, Types } from '@ohif/core'; import init from './init'; import getCommandsModule from './commandsModule'; @@ -16,10 +16,11 @@ import ToolGroupService from './services/ToolGroupService'; import SyncGroupService from './services/SyncGroupService'; import SegmentationService from './services/SegmentationService'; import CornerstoneCacheService from './services/CornerstoneCacheService'; +import CornerstoneViewportService from './services/ViewportService/CornerstoneViewportService'; +import * as CornerstoneExtensionTypes from './types'; import { toolNames } from './initCornerstoneTools'; import { getEnabledElement, reset as enabledElementReset } from './state'; -import CornerstoneViewportService from './services/ViewportService/CornerstoneViewportService'; import dicomLoaderService from './utils/dicomLoaderService'; import { registerColormap } from './utils/colormap/transferFunctionHelpers'; @@ -72,18 +73,11 @@ const cornerstoneExtension: Types.Extensions.Extension = { props: Types.Extensions.ExtensionParams ): Promise { const { servicesManager } = props; - // Todo: we should be consistent with how services get registered. Use REGISTRATION static method for all - servicesManager.registerService( - CornerstoneViewportService(servicesManager) - ); - servicesManager.registerService( - ToolGroupService.REGISTRATION(servicesManager) - ); - servicesManager.registerService(SyncGroupService(servicesManager)); - servicesManager.registerService(SegmentationService(servicesManager)); - servicesManager.registerService( - CornerstoneCacheService.REGISTRATION(servicesManager) - ); + servicesManager.registerService(CornerstoneViewportService.REGISTRATION); + servicesManager.registerService(ToolGroupService.REGISTRATION); + servicesManager.registerService(SyncGroupService.REGISTRATION); + servicesManager.registerService(SegmentationService.REGISTRATION); + servicesManager.registerService(CornerstoneCacheService.REGISTRATION); return init.call(this, props); }, @@ -145,5 +139,5 @@ const cornerstoneExtension: Types.Extensions.Extension = { }; export type { PublicViewportOptions }; -export { measurementMappingUtils }; +export { measurementMappingUtils, CornerstoneExtensionTypes }; export default cornerstoneExtension; diff --git a/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts b/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts index 56c8d6fa5..7eb2d6751 100644 --- a/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts +++ b/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts @@ -1,4 +1,4 @@ -import { ServicesManager } from '@ohif/core'; +import { ServicesManager, Types } from '@ohif/core'; import { cache as cs3DCache, Enums, volumeLoader } from '@cornerstonejs/core'; import getCornerstoneViewportType from '../../utils/getCornerstoneViewportType'; @@ -10,20 +10,21 @@ import { const VOLUME_LOADER_SCHEME = 'cornerstoneStreamingImageVolume'; class CornerstoneCacheService { - static REGISTRATION = (serviceManager: ServicesManager) => { - return { - name: 'cornerstoneCacheService', - altName: 'CornerstoneCacheService', - create: ({ configuration = {} }) => { - return new CornerstoneCacheService(serviceManager); - }, - }; + static REGISTRATION = { + name: 'cornerstoneCacheService', + altName: 'CornerstoneCacheService', + create: ({ + servicesManager, + }: Types.Extensions.ExtensionParams): CornerstoneCacheService => { + return new CornerstoneCacheService(servicesManager); + }, }; stackImageIds: Map = new Map(); volumeImageIds: Map = new Map(); + readonly servicesManager: ServicesManager; - constructor(servicesManager) { + constructor(servicesManager: ServicesManager) { this.servicesManager = servicesManager; } diff --git a/extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts b/extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts index 658ee816f..d4c25bee4 100644 --- a/extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts +++ b/extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts @@ -1,5 +1,6 @@ import cloneDeep from 'lodash.clonedeep'; +import { Types as OhifTypes, ServicesManager, PubSubService } from '@ohif/core'; import { cache, eventTarget, @@ -16,7 +17,6 @@ import { Types as cstTypes, utilities as cstUtils, } from '@cornerstonejs/tools'; -import { pubSubServiceInterface } from '@ohif/core'; import isEqual from 'lodash.isequal'; import { easeInOutBell } from '../../utils/transitions'; import { @@ -47,19 +47,26 @@ const EVENTS = { const VALUE_TYPES = {}; -class SegmentationService { - listeners = {}; +class SegmentationService extends PubSubService { + static REGISTRATION = { + name: 'segmentationService', + altName: 'SegmentationService', + create: ({ + servicesManager, + }: OhifTypes.Extensions.ExtensionParams): SegmentationService => { + return new SegmentationService({ servicesManager }); + }, + }; + segmentations: Record; - servicesManager = null; + readonly servicesManager: ServicesManager; highlightIntervalId = null; - _broadcastEvent: (eventName: string, callbackProps: any) => void; readonly EVENTS = EVENTS; constructor({ servicesManager }) { + super(EVENTS); this.segmentations = {}; - this.listeners = {}; - Object.assign(this, pubSubServiceInterface); this.servicesManager = servicesManager; this._initSegmentationService(); diff --git a/extensions/cornerstone/src/services/SegmentationService/index.js b/extensions/cornerstone/src/services/SegmentationService/index.js index 7b89d9bec..848c25ef9 100644 --- a/extensions/cornerstone/src/services/SegmentationService/index.js +++ b/extensions/cornerstone/src/services/SegmentationService/index.js @@ -1,11 +1,3 @@ import SegmentationService from './SegmentationService'; -export default function ExtendedSegmentationService(servicesManager) { - return { - name: 'segmentationService', - altName: 'SegmentationService', - create: ({ configuration = {} }) => { - return new SegmentationService({ servicesManager }); - }, - }; -} +export default SegmentationService; diff --git a/extensions/cornerstone/src/services/SyncGroupService/SyncGroupService.ts b/extensions/cornerstone/src/services/SyncGroupService/SyncGroupService.ts index 6acfce70a..39e919fc5 100644 --- a/extensions/cornerstone/src/services/SyncGroupService/SyncGroupService.ts +++ b/extensions/cornerstone/src/services/SyncGroupService/SyncGroupService.ts @@ -4,7 +4,7 @@ import { Synchronizer, } from '@cornerstonejs/tools'; -import { pubSubServiceInterface } from '@ohif/core'; +import { pubSubServiceInterface, Types, ServicesManager } from '@ohif/core'; const EVENTS = { TOOL_GROUP_CREATED: 'event::cornerstone::syncgroupservice:toolgroupcreated', @@ -37,7 +37,17 @@ const asSyncGroup = (syncGroup: string | SyncGroup): SyncGroup => typeof syncGroup === 'string' ? { type: syncGroup } : syncGroup; export default class SyncGroupService { - serviceManager: any; + static REGISTRATION = { + name: 'syncGroupService', + altName: 'SyncGroupService', + create: ({ + servicesManager, + }: Types.Extensions.ExtensionParams): SyncGroupService => { + return new SyncGroupService(servicesManager); + }, + }; + + servicesManager: ServicesManager; listeners: { [key: string]: (...args: any[]) => void } = {}; EVENTS: { [key: string]: string }; synchronizerCreators: Record = { @@ -47,8 +57,8 @@ export default class SyncGroupService { [STACKIMAGE]: synchronizers.createStackImageSynchronizer, }; - constructor(serviceManager) { - this.serviceManager = serviceManager; + constructor(serviceManager: ServicesManager) { + this.servicesManager = serviceManager; this.listeners = {}; this.EVENTS = EVENTS; // diff --git a/extensions/cornerstone/src/services/SyncGroupService/index.js b/extensions/cornerstone/src/services/SyncGroupService/index.js index 64cb989fe..1e0a21819 100644 --- a/extensions/cornerstone/src/services/SyncGroupService/index.js +++ b/extensions/cornerstone/src/services/SyncGroupService/index.js @@ -1,11 +1,3 @@ import SyncGroupService from './SyncGroupService'; -export default function ExtendedSyncGroupService(serviceManager) { - return { - altName: 'SyncGroupService', - name: 'syncGroupService', - create: ({ configuration = {} }) => { - return new SyncGroupService(serviceManager); - }, - }; -} +export default SyncGroupService; diff --git a/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts b/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts index f0f0bf4be..4f5512ecf 100644 --- a/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts +++ b/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts @@ -1,6 +1,6 @@ import { ToolGroupManager, Enums, Types } from '@cornerstonejs/tools'; -import { pubSubServiceInterface } from '@ohif/core'; +import { Types as OhifTypes, pubSubServiceInterface } from '@ohif/core'; const EVENTS = { VIEWPORT_ADDED: 'event::cornerstone::toolgroupservice:viewportadded', @@ -20,14 +20,14 @@ type Tools = { }; export default class ToolGroupService { - public static REGISTRATION = serviceManager => { - return { - name: 'toolGroupService', - altName: 'ToolGroupService', - create: ({ configuration = {} }) => { - return new ToolGroupService(serviceManager); - }, - }; + public static REGISTRATION = { + name: 'toolGroupService', + altName: 'ToolGroupService', + create: ({ + servicesManager, + }: OhifTypes.Extensions.ExtensionParams): ToolGroupService => { + return new ToolGroupService(servicesManager); + }, }; serviceManager: any; diff --git a/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts b/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts index 946dee124..a99083d8b 100644 --- a/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts +++ b/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts @@ -1,4 +1,5 @@ -import { PubSubService } from '@ohif/core'; +import { PubSubService, ServicesManager } from '@ohif/core'; +import * as OhifTypes from '@ohif/core/types'; import { RenderingEngine, StackViewport, @@ -43,6 +44,16 @@ const EVENTS = { */ class CornerstoneViewportService extends PubSubService implements IViewportService { + static REGISTRATION = { + name: 'cornerstoneViewportService', + altName: 'CornerstoneViewportService', + create: ({ + servicesManager, + }: OhifTypes.Extensions.ExtensionParams): CornerstoneViewportService => { + return new CornerstoneViewportService(servicesManager); + }, + }; + renderingEngine: Types.IRenderingEngine | null; viewportsInfo: Map = new Map(); viewportsById: Map = new Map(); @@ -55,7 +66,7 @@ class CornerstoneViewportService extends PubSubService resizeRefreshMode: 'debounce'; servicesManager = null; - constructor(servicesManager) { + constructor(servicesManager: ServicesManager) { super(EVENTS); this.renderingEngine = null; this.viewportGridResizeObserver = null; @@ -71,7 +82,7 @@ class CornerstoneViewportService extends PubSubService viewportIndex: number, viewportOptions: PublicViewportOptions, elementRef: HTMLDivElement - ) { + ): void { // Use the provided viewportId // Not providing a viewportId is frowned upon because it does weird things // on moving them around, but it does mostly work. @@ -855,14 +866,4 @@ class CornerstoneViewportService extends PubSubService } } -export default function CornerstoneViewportServiceRegistration(serviceManager) { - return { - name: 'cornerstoneViewportService', - altName: 'CornerstoneViewportService', - create: ({ configuration = {} }) => { - return new CornerstoneViewportService(serviceManager); - }, - }; -} - -export { CornerstoneViewportService, CornerstoneViewportServiceRegistration }; +export default CornerstoneViewportService; diff --git a/extensions/cornerstone/src/types/CornerstoneServices.ts b/extensions/cornerstone/src/types/CornerstoneServices.ts new file mode 100644 index 000000000..2f52dc9ff --- /dev/null +++ b/extensions/cornerstone/src/types/CornerstoneServices.ts @@ -0,0 +1,16 @@ +import { Types } from '@ohif/core'; +import ToolGroupService from './services/ToolGroupService'; +import SyncGroupService from './services/SyncGroupService'; +import SegmentationService from './services/SegmentationService'; +import CornerstoneCacheService from './services/CornerstoneCacheService'; +import CornerstoneViewportService from './services/ViewportService/CornerstoneViewportService'; + +interface CornerstoneServices extends Types.Services { + cornerstoneViewportService: CornerstoneViewportService; + toolGroupService: ToolGroupService; + syncGroupService: SyncGroupService; + segmentationService: SegmentationService; + cornerstoneCacheService: CornerstoneCacheService; +} + +export default CornerstoneServices; diff --git a/extensions/cornerstone/src/types/index.ts b/extensions/cornerstone/src/types/index.ts index 8c8e32e98..6c729817d 100644 --- a/extensions/cornerstone/src/types/index.ts +++ b/extensions/cornerstone/src/types/index.ts @@ -1,5 +1,7 @@ import * as CornerstoneCacheService from './CornerstoneCacheService' +import CornerstoneServices from './CornerstoneServices'; export type { - CornerstoneCacheService + CornerstoneCacheService, + CornerstoneServices, } diff --git a/extensions/default/src/CustomizeableContextMenu/index.ts b/extensions/default/src/CustomizeableContextMenu/index.ts index d630bcad9..7dc08dd3d 100644 --- a/extensions/default/src/CustomizeableContextMenu/index.ts +++ b/extensions/default/src/CustomizeableContextMenu/index.ts @@ -1,5 +1,5 @@ import ContextMenuController from './ContextMenuController'; -import ContextMenuItemsBuilder from './ContextMenuItemsBuilder'; +import * as ContextMenuItemsBuilder from './ContextMenuItemsBuilder'; import defaultContextMenu from './defaultContextMenu'; import * as CustomizeableContextMenuTypes from './types'; diff --git a/platform/core/package.json b/platform/core/package.json index cb97a9eab..afd26b6cb 100644 --- a/platform/core/package.json +++ b/platform/core/package.json @@ -7,6 +7,7 @@ "repository": "OHIF/Viewers", "main": "dist/index.umd.js", "module": "src/index.ts", + "types": "src/types/index.ts", "sideEffects": "false", "publishConfig": { "access": "public" diff --git a/platform/core/src/extensions/ExtensionManager.ts b/platform/core/src/extensions/ExtensionManager.ts index 188da5add..9c26d7370 100644 --- a/platform/core/src/extensions/ExtensionManager.ts +++ b/platform/core/src/extensions/ExtensionManager.ts @@ -37,9 +37,12 @@ export interface ExtensionParams extends ExtensionConstructor { export interface Extension { id: string; preRegistration?: (p: ExtensionParams) => Promise | void; - onModeExit?: () => void; getHangingProtocolModule?: (p: ExtensionParams) => unknown; getCommandsModule?: (p: ExtensionParams) => CommandsModule; + getViewportModule?: (p: ExtensionParams) => unknown; + getUtilityModule?: (p: ExtensionParams) => unknown; + onModeEnter?: () => void; + onModeExit?: () => void; } export type ExtensionRegister = { diff --git a/platform/core/src/services/UIModalService/index.js b/platform/core/src/services/UIModalService/index.js deleted file mode 100644 index babeb6e5c..000000000 --- a/platform/core/src/services/UIModalService/index.js +++ /dev/null @@ -1,91 +0,0 @@ -/** - * UI Modal - * - * @typedef {Object} ModalProps - * @property {ReactElement|HTMLElement} [content=null] Modal content. - * @property {Object} [contentProps=null] Modal content props. - * @property {boolean} [shouldCloseOnEsc=false] Modal is dismissible via the esc key. - * @property {boolean} [isOpen=true] Make the Modal visible or hidden. - * @property {boolean} [closeButton=true] Should the modal body render the close button. - * @property {string} [title=null] Should the modal render the title independently of the body content. - * @property {string} [customClassName=null] The custom class to style the modal. - */ - -const name = 'uiModalService'; - -const publicAPI = { - name, - hide: _hide, - show: _show, - setServiceImplementation, -}; - -const serviceImplementation = { - _hide: () => console.warn('hide() NOT IMPLEMENTED'), - _show: () => console.warn('show() NOT IMPLEMENTED'), -}; - -/** - * Show a new UI modal; - * - * @param {ModalProps} props { content, contentProps, shouldCloseOnEsc, isOpen, closeButton, title, customClassName } - */ -function _show({ - content = null, - contentProps = null, - shouldCloseOnEsc = true, - isOpen = true, - closeButton = true, - title = null, - customClassName = null, -}) { - return serviceImplementation._show({ - content, - contentProps, - shouldCloseOnEsc, - isOpen, - closeButton, - title, - customClassName, - }); -} - -/** - * Hides/dismisses the modal, if currently shown - * - * @returns void - */ -function _hide() { - return serviceImplementation._hide(); -} - -/** - * - * - * @param {*} { - * hide: hideImplementation, - * show: showImplementation, - * } - */ -function setServiceImplementation({ - hide: hideImplementation, - show: showImplementation, -}) { - if (hideImplementation) { - serviceImplementation._hide = hideImplementation; - } - if (showImplementation) { - serviceImplementation._show = showImplementation; - } -} - -// TODO - export TS Type -export default { - REGISTRATION: { - name, - altName: 'UIModalService', - create: ({ configuration = {} }) => { - return publicAPI; - }, - }, -}; diff --git a/platform/core/src/services/UIModalService/index.ts b/platform/core/src/services/UIModalService/index.ts new file mode 100644 index 000000000..3b33d3806 --- /dev/null +++ b/platform/core/src/services/UIModalService/index.ts @@ -0,0 +1,87 @@ +/** + * UI Modal + * + * @typedef {Object} ModalProps + * @property {ReactElement|HTMLElement} [content=null] Modal content. + * @property {Object} [contentProps=null] Modal content props. + * @property {boolean} [shouldCloseOnEsc=false] Modal is dismissible via the esc key. + * @property {boolean} [isOpen=true] Make the Modal visible or hidden. + * @property {boolean} [closeButton=true] Should the modal body render the close button. + * @property {string} [title=null] Should the modal render the title independently of the body content. + * @property {string} [customClassName=null] The custom class to style the modal. + */ + +const name = 'uiModalService'; + +const serviceImplementation = { + _hide: () => console.warn('hide() NOT IMPLEMENTED'), + _show: () => console.warn('show() NOT IMPLEMENTED'), +}; + +class UIModalService { + static REGISTRATION = { + name, + altName: 'UIModalService', + create: (): UIModalService => { + return new UIModalService(); + }, + }; + + readonly name = name; + + /** + * Show a new UI modal; + * + * @param {ModalProps} props { content, contentProps, shouldCloseOnEsc, isOpen, closeButton, title, customClassName } + */ + show({ + content = null, + contentProps = null, + shouldCloseOnEsc = true, + isOpen = true, + closeButton = true, + title = null, + customClassName = null, + }) { + return serviceImplementation._show({ + content, + contentProps, + shouldCloseOnEsc, + isOpen, + closeButton, + title, + customClassName, + }); + } + + /** + * Hides/dismisses the modal, if currently shown + * + * @returns void + */ + hide() { + return serviceImplementation._hide(); + } + + /** + * + * + * @param {*} { + * hide: hideImplementation, + * show: showImplementation, + * } + */ + setServiceImplementation({ + hide: hideImplementation, + show: showImplementation, + }) { + if (hideImplementation) { + serviceImplementation._hide = hideImplementation; + } + if (showImplementation) { + serviceImplementation._show = showImplementation; + } + } +} + +export default UIModalService; diff --git a/platform/core/src/services/UINotificationService/index.js b/platform/core/src/services/UINotificationService/index.js deleted file mode 100644 index a21033759..000000000 --- a/platform/core/src/services/UINotificationService/index.js +++ /dev/null @@ -1,101 +0,0 @@ -/** - * A UI Notification - * - * @typedef {Object} Notification - * @property {string} title - - * @property {string} message - - * @property {number} [duration=5000] - in ms - * @property {string} [position="bottomRight"] -"topLeft" | "topCenter | "topRight" | "bottomLeft" | "bottomCenter" | "bottomRight" - * @property {string} [type="info"] - "info" | "error" | "warning" | "success" - * @property {boolean} [autoClose=true] - */ - -const name = 'uiNotificationService'; - -const serviceShowRequestQueue = []; - -const publicAPI = { - name, - hide: _hide, - show: _show, - setServiceImplementation, -}; - -const serviceImplementation = { - _hide: () => console.warn('hide() NOT IMPLEMENTED'), - _show: showArguments => { - serviceShowRequestQueue.push(showArguments); - - console.warn('show() NOT IMPLEMENTED'); - }, -}; - -/** - * Create and show a new UI notification; returns the - * ID of the created notification. - * - * @param {Notification} notification { title, message, duration, position, type, autoClose} - * @returns {number} id - */ -function _show({ - title, - message, - duration = 5000, - position = 'bottomRight', - type = 'info', - autoClose = true, -}) { - return serviceImplementation._show({ - title, - message, - duration, - position, - type, - autoClose, - }); -} - -/** - * Hides/dismisses the notification, if currently shown - * - * @param {number} id - id of the notification to hide/dismiss - * @returns undefined - */ -function _hide(id) { - return serviceImplementation._hide({ id }); -} - -/** - * - * - * @param {*} { - * hide: hideImplementation, - * show: showImplementation, - * } - */ -function setServiceImplementation({ - hide: hideImplementation, - show: showImplementation, -}) { - if (hideImplementation) { - serviceImplementation._hide = hideImplementation; - } - if (showImplementation) { - serviceImplementation._show = showImplementation; - - while (serviceShowRequestQueue.length > 0) { - const showArguments = serviceShowRequestQueue.pop(); - serviceImplementation._show(showArguments); - } - } -} - -export default { - REGISTRATION: { - name, - altName: 'UINotificationService', - create: ({ configuration = {} }) => { - return publicAPI; - }, - }, -}; diff --git a/platform/core/src/services/UINotificationService/index.ts b/platform/core/src/services/UINotificationService/index.ts new file mode 100644 index 000000000..78a2882af --- /dev/null +++ b/platform/core/src/services/UINotificationService/index.ts @@ -0,0 +1,94 @@ +/** + * A UI Notification + * + * @typedef {Object} Notification + * @property {string} title - + * @property {string} message - + * @property {number} [duration=5000] - in ms + * @property {string} [position="bottomRight"] -"topLeft" | "topCenter | "topRight" | "bottomLeft" | "bottomCenter" | "bottomRight" + * @property {string} [type="info"] - "info" | "error" | "warning" | "success" + * @property {boolean} [autoClose=true] + */ + +const serviceShowRequestQueue = []; + +const serviceImplementation = { + _hide: () => console.warn('hide() NOT IMPLEMENTED'), + _show: showArguments => { + serviceShowRequestQueue.push(showArguments); + + console.warn('show() NOT IMPLEMENTED'); + }, +}; + +class UINotificationService { + static REGISTRATION = { + name: 'uiNotificationService', + altName: 'UINotificationService', + create: (): UINotificationService => { + return new UINotificationService(); + }, + }; + + /** + * + * + * @param {*} { + * hide: hideImplementation, + * show: showImplementation, + * } + */ + public setServiceImplementation({ + hide: hideImplementation, + show: showImplementation, + }): void { + if (hideImplementation) { + serviceImplementation._hide = hideImplementation; + } + if (showImplementation) { + serviceImplementation._show = showImplementation; + + while (serviceShowRequestQueue.length > 0) { + const showArguments = serviceShowRequestQueue.pop(); + serviceImplementation._show(showArguments); + } + } + } + + /** + * Hides/dismisses the notification, if currently shown + * + * @param {number} id - id of the notification to hide/dismiss + * @returns undefined + */ + public hide(id: string) { + return serviceImplementation._hide({ id }); + } + + /** + * Create and show a new UI notification; returns the + * ID of the created notification. + * + * @param {Notification} notification { title, message, duration, position, type, autoClose} + * @returns {number} id + */ + show({ + title, + message, + duration = 5000, + position = 'bottomRight', + type = 'info', + autoClose = true, + }) { + return serviceImplementation._show({ + title, + message, + duration, + position, + type, + autoClose, + }); + } +} + +export default UINotificationService; diff --git a/platform/core/src/types/Services.ts b/platform/core/src/types/Services.ts index ca73361ca..abc6b09be 100644 --- a/platform/core/src/types/Services.ts +++ b/platform/core/src/types/Services.ts @@ -6,6 +6,8 @@ import { ToolbarService, DisplaySetService, StateSyncService, + UINotificationService, + UIModalService, } from '../services'; /** @@ -22,8 +24,8 @@ export default interface Services { cornerstoneViewportService?: Record; uiDialogService?: Record; toolGroupService?: Record; - uiNotificationService?: Record; - uiModalService?: Record; + uiNotificationService?: UINotificationService; + uiModalService?: UIModalService; uiViewportDialogService?: Record; viewportGridService?: ViewportGridService; syncGroupService?: Record; diff --git a/platform/ui/src/types/index.ts b/platform/ui/src/types/index.ts index 78b560486..5d0729fbe 100644 --- a/platform/ui/src/types/index.ts +++ b/platform/ui/src/types/index.ts @@ -1,6 +1,6 @@ import PropTypes from 'prop-types'; import ThumbnailType from './ThumbnailType'; -import { PresentationIds } from '../contextProviders/getPresentationIds'; +import type { PresentationIds } from '../contextProviders/getPresentationIds'; // A few miscellaneous types declared inline here. From c508a2b6bce4d2d8c151cd4492a6a7dac7e0233c Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Tue, 18 Apr 2023 11:55:25 -0400 Subject: [PATCH 11/54] feat: Add a new hanging protocol @ohif/mn (#3305) * feat: Add a new hanging protocol @ohif/mn * Add @ohif/seg example * PR comments and a couple more fixes to make things cleaner * PR comment * Added an example to cause the PR checks to rerun --- .../src/getHangingProtocolModule.ts | 78 +++++++ .../cornerstone-dicom-seg/src/index.tsx | 3 + .../src/getHangingProtocolModule.ts | 9 +- extensions/default/src/commandsModule.ts | 2 +- .../default/src/getHangingProtocolModule.js | 212 +----------------- .../hp/hpMN.ts => default/src/hpMNGrid.ts} | 33 +-- .../findingsContextMenu.ts | 4 +- extensions/test-extension/src/hp/index.ts | 17 -- extensions/test-extension/src/index.tsx | 16 -- modes/basic-test-mode/src/toolbarButtons.js | 8 +- .../HangingProtocolService.ts | 14 +- .../isDisplaySetFromUrl.ts | 4 +- .../numberOfDisplaySetsWithImages.ts | 0 .../seriesDescriptionsFromDisplaySets.ts | 0 .../customization/HangingProtocol.spec.js | 2 +- .../customization/OHIFDoubleClick.spec.js | 2 +- platform/viewer/public/config/e2e.js | 138 ++++-------- 17 files changed, 184 insertions(+), 358 deletions(-) create mode 100644 extensions/cornerstone-dicom-seg/src/getHangingProtocolModule.ts rename extensions/{test-extension/src/hp/hpMN.ts => default/src/hpMNGrid.ts} (88%) delete mode 100644 extensions/test-extension/src/hp/index.ts rename platform/core/src/services/HangingProtocolService/{ => custom-attribute}/isDisplaySetFromUrl.ts (94%) rename {extensions/test-extension/src => platform/core/src/services/HangingProtocolService}/custom-attribute/numberOfDisplaySetsWithImages.ts (100%) rename {extensions/test-extension/src => platform/core/src/services/HangingProtocolService}/custom-attribute/seriesDescriptionsFromDisplaySets.ts (100%) diff --git a/extensions/cornerstone-dicom-seg/src/getHangingProtocolModule.ts b/extensions/cornerstone-dicom-seg/src/getHangingProtocolModule.ts new file mode 100644 index 000000000..0a2f888e4 --- /dev/null +++ b/extensions/cornerstone-dicom-seg/src/getHangingProtocolModule.ts @@ -0,0 +1,78 @@ +import { Types } from '@ohif/core'; + +const segProtocol: Types.HangingProtocol.Protocol = { + id: '@ohif/seg', + // Don't store this hanging protocol as it applies to the currently active + // display set by default + // cacheId: null, + hasUpdatedPriorsInformation: false, + name: 'Segmentations', + // Just apply this one when specifically listed + protocolMatchingRules: [], + toolGroupIds: ['default'], + // -1 would be used to indicate active only, whereas other values are + // the number of required priors referenced - so 0 means active with + // 0 or more priors. + numberOfPriorsReferenced: 0, + // Default viewport is used to define the viewport when + // additional viewports are added using the layout tool + defaultViewport: { + viewportOptions: { + viewportType: 'stack', + toolGroupId: 'default', + allowUnmatchedView: true, + }, + displaySets: [ + { + id: 'segDisplaySetId', + matchedDisplaySetsIndex: -1, + }, + ], + }, + displaySetSelectors: { + segDisplaySetId: { + seriesMatchingRules: [ + { + attribute: 'Modality', + constraint: { + equals: 'SEG', + }, + }, + ], + }, + }, + stages: [ + { + name: 'Segmentations', + viewportStructure: { + layoutType: 'grid', + properties: { + rows: 1, + columns: 1, + }, + }, + viewports: [ + { + viewportOptions: { allowUnmatchedView: true }, + displaySets: [ + { + id: 'segDisplaySetId', + }, + ], + }, + ], + }, + ], +}; + +function getHangingProtocolModule() { + return [ + { + name: segProtocol.id, + protocol: segProtocol, + }, + ]; +} + +export default getHangingProtocolModule; +export { segProtocol }; diff --git a/extensions/cornerstone-dicom-seg/src/index.tsx b/extensions/cornerstone-dicom-seg/src/index.tsx index fde3d95a9..b77fb6677 100644 --- a/extensions/cornerstone-dicom-seg/src/index.tsx +++ b/extensions/cornerstone-dicom-seg/src/index.tsx @@ -5,6 +5,7 @@ import { Types } from '@ohif/core'; import getSopClassHandlerModule from './getSopClassHandlerModule'; import PanelSegmentation from './panels/PanelSegmentation'; +import getHangingProtocolModule from './getHangingProtocolModule'; const Component = React.lazy(() => { return import( @@ -79,6 +80,8 @@ const extension = { * Examples include the default sop class handler provided by the default extension */ getSopClassHandlerModule, + + getHangingProtocolModule, }; export default extension; diff --git a/extensions/cornerstone/src/getHangingProtocolModule.ts b/extensions/cornerstone/src/getHangingProtocolModule.ts index 2c21e0ab1..985c60ea6 100644 --- a/extensions/cornerstone/src/getHangingProtocolModule.ts +++ b/extensions/cornerstone/src/getHangingProtocolModule.ts @@ -1,11 +1,12 @@ import { Types } from '@ohif/core'; const mpr: Types.HangingProtocol.Protocol = { + id: 'mpr', + name: 'Multi-Planar Reconstruction', locked: true, hasUpdatedPriorsInformation: false, - name: 'mpr', - createdDate: '2021-02-23T19:22:08.894Z', - modifiedDate: '2023-02-17', + createdDate: '2021-02-23', + modifiedDate: '2023-04-03', availableTo: {}, editableBy: {}, // Unknown number of priors referenced - so just match any study @@ -303,7 +304,7 @@ const mprAnd3DVolumeViewport = { function getHangingProtocolModule() { return [ { - name: 'mpr', + name: mpr.id, protocol: mpr, }, { diff --git a/extensions/default/src/commandsModule.ts b/extensions/default/src/commandsModule.ts index a14563e93..73b54b5df 100644 --- a/extensions/default/src/commandsModule.ts +++ b/extensions/default/src/commandsModule.ts @@ -171,7 +171,7 @@ const commandsModule = ({ reset = false, }: HangingProtocolParams): boolean => { try { - // Stores in the state the reuseID to displaySetUID mapping + // Stores in the state the display set selector id to displaySetUID mapping // Pass in viewportId for the active viewport. This item will get set as // the activeViewportId const state = viewportGridService.getState(); diff --git a/extensions/default/src/getHangingProtocolModule.js b/extensions/default/src/getHangingProtocolModule.js index b575d9086..5875e8e76 100644 --- a/extensions/default/src/getHangingProtocolModule.js +++ b/extensions/default/src/getHangingProtocolModule.js @@ -1,3 +1,5 @@ +import hpMNGrid from './hpMNGrid'; + const defaultProtocol = { id: 'default', locked: true, @@ -92,211 +94,6 @@ const defaultProtocol = { ], createdDate: '2021-02-23T18:32:42.850Z', }, - - // This is an example of a 2x2 layout that requires at least 2 viewports - // filled to be navigatable to - { - name: '2x2', - // Indicate that the number of viewports needed is 2 filled viewports, - // but that 4 viewports are preferred. - stageActivation: { - enabled: { - minViewportsMatched: 4, - }, - passive: { - minViewportsMatched: 2, - }, - }, - - viewportStructure: { - layoutType: 'grid', - properties: { - rows: 2, - columns: 2, - }, - }, - viewports: [ - { - viewportOptions: { - toolGroupId: 'default', - }, - displaySets: [ - { - id: 'defaultDisplaySetId', - matchedDisplaySetsIndex: 3, - }, - ], - }, - { - viewportOptions: { - toolGroupId: 'default', - }, - displaySets: [ - { - id: 'defaultDisplaySetId', - matchedDisplaySetsIndex: 2, - }, - ], - }, - { - viewportOptions: { - toolGroupId: 'default', - }, - displaySets: [ - { - id: 'defaultDisplaySetId', - matchedDisplaySetsIndex: 1, - }, - ], - }, - { - viewportOptions: {}, - displaySets: [ - { - id: 'defaultDisplaySetId', - matchedDisplaySetsIndex: 0, - }, - ], - }, - ], - }, - - { - name: '3x1', - // Indicate that the number of viewports needed is 2 filled viewports, - // but that 4 viewports are preferred. - stageActivation: { - enabled: { - minViewportsMatched: 3, - }, - }, - - viewportStructure: { - layoutType: 'grid', - properties: { - rows: 1, - columns: 3, - }, - }, - viewports: [ - { - viewportOptions: { - toolGroupId: 'default', - }, - displaySets: [ - { - id: 'defaultDisplaySetId', - matchedDisplaySetsIndex: 2, - }, - ], - }, - { - viewportOptions: { - toolGroupId: 'default', - }, - displaySets: [ - { - id: 'defaultDisplaySetId', - matchedDisplaySetsIndex: 1, - }, - ], - }, - { - viewportOptions: {}, - displaySets: [ - { - id: 'defaultDisplaySetId', - }, - ], - }, - ], - }, - - // This is an example of a layout with more than one element in it - // It can be navigated to using , and . (prev/next stage) - { - name: '2x1', - // Indicate that the number of viewports needed is 1 filled viewport, - // but that 2 viewports are preferred. - stageActivation: { - enabled: { - minViewportsMatched: 3, - }, - }, - - viewportStructure: { - layoutType: 'grid', - properties: { - rows: 1, - columns: 2, - }, - }, - viewports: [ - { - viewportOptions: { - toolGroupId: 'default', - // initialImageOptions: { - // index: 180, - // preset: 'middle', // 'first', 'last', 'middle' - // }, - }, - displaySets: [ - { - id: 'defaultDisplaySetId', - // Shows the second index of this image set - matchedDisplaySetsIndex: 1, - }, - ], - }, - { - viewportOptions: {}, - displaySets: [ - { - id: 'defaultDisplaySetId', - }, - ], - }, - ], - }, - - { - name: '2x1', - // Indicate that the number of viewports needed is 1 filled viewport, - // but that 2 viewports are preferred. - stageActivation: { - enabled: { - minViewportsMatched: 3, - }, - }, - - viewportStructure: { - layoutType: 'grid', - properties: { - rows: 2, - columns: 1, - }, - }, - viewports: [ - { - viewportOptions: {}, - displaySets: [ - { - id: 'defaultDisplaySetId', - // Shows the second index of this image set - matchedDisplaySetsIndex: 1, - }, - ], - }, - { - viewportOptions: {}, - displaySets: [ - { - id: 'defaultDisplaySetId', - }, - ], - }, - ], - }, ], }; @@ -306,6 +103,11 @@ function getHangingProtocolModule() { name: defaultProtocol.id, protocol: defaultProtocol, }, + // Create a MxN hanging protocol available by default + { + name: hpMNGrid.id, + protocol: hpMNGrid, + }, ]; } diff --git a/extensions/test-extension/src/hp/hpMN.ts b/extensions/default/src/hpMNGrid.ts similarity index 88% rename from extensions/test-extension/src/hp/hpMN.ts rename to extensions/default/src/hpMNGrid.ts index fc8fe4538..2e3206615 100644 --- a/extensions/test-extension/src/hp/hpMN.ts +++ b/extensions/default/src/hpMNGrid.ts @@ -1,24 +1,23 @@ import { Types } from '@ohif/core'; /** - * This hanging protocol has multiple stages, which are enabled when - * there are enough display sets with images to fill the stage, and - * are passive when there is at least one display set. - * Enabled display sets are navigated to by default, while passive ones - * are navigated to manually using the ctrl+end keyboard shortcut. + * This hanging protocol can be activated on the primary mode by directly + * referencing it in a URL or by directly including it within a mode, e.g.: + * `&hangingProtocolId=@ohif/mnGrid` added to the viewer URL + * It is not included in the viewer mode by default. */ const hpMN: Types.HangingProtocol.Protocol = { hasUpdatedPriorsInformation: false, - id: '@ohif/hp-extension.mn', - description: 'Has various hanging protocol layouts for use in testing', + id: '@ohif/mnGrid', + description: 'Has various hanging protocol grid layouts', name: '2x2', protocolMatchingRules: [ { id: 'OneOrMoreSeries', - weight: 1, + weight: 25, attribute: 'numberOfDisplaySetsWithImages', constraint: { - greaterThan: 1, + greaterThan: 0, }, }, ], @@ -32,6 +31,15 @@ const hpMN: Types.HangingProtocol.Protocol = { greaterThan: { value: 0 }, }, }, + // This display set will select the specified items by preference + // It has no affect if nothing is specified in the URL. + { + attribute: 'isDisplaySetFromUrl', + weight: 10, + constraint: { + equals: true, + }, + }, ], }, }, @@ -142,7 +150,6 @@ const hpMN: Types.HangingProtocol.Protocol = { displaySets: [ { id: 'defaultDisplaySetId', - reuseId: '0-0', }, ], }, @@ -153,9 +160,8 @@ const hpMN: Types.HangingProtocol.Protocol = { }, displaySets: [ { + id: 'defaultDisplaySetId', matchedDisplaySetsIndex: 1, - id: 'defaultDisplaySetId', - reuseId: '1-0', }, ], }, @@ -166,9 +172,8 @@ const hpMN: Types.HangingProtocol.Protocol = { }, displaySets: [ { - matchedDisplaySetsIndex: 2, id: 'defaultDisplaySetId', - reuseId: '0-1', + matchedDisplaySetsIndex: 2, }, ], }, diff --git a/extensions/test-extension/src/custom-context-menu/findingsContextMenu.ts b/extensions/test-extension/src/custom-context-menu/findingsContextMenu.ts index ebdd32eef..1a0a22069 100644 --- a/extensions/test-extension/src/custom-context-menu/findingsContextMenu.ts +++ b/extensions/test-extension/src/custom-context-menu/findingsContextMenu.ts @@ -38,12 +38,12 @@ const findingsContextMenu = { }, // The example below shows how to include a delegating sub-menu, - // Only available on the @ohif/hp-extension.mn hanging protocol + // Only available on the @ohif/mnGrid hanging protocol // To demonstrate, select the 3x1 layout from the protocol menu // and right click on a measurement. { label: 'IncludeSubMenu', - selector: ({ protocol }) => protocol?.id === '@ohif/hp-extension.mn', + selector: ({ protocol }) => protocol?.id === '@ohif/mnGrid', delegating: true, subMenu: 'orientationSelectionSubMenu', }, diff --git a/extensions/test-extension/src/hp/index.ts b/extensions/test-extension/src/hp/index.ts deleted file mode 100644 index a1b0c22c2..000000000 --- a/extensions/test-extension/src/hp/index.ts +++ /dev/null @@ -1,17 +0,0 @@ -import hpMN from './hpMN'; - -const hangingProtocols = [ - { - name: '@ohif/hp-extension.mn', - protocol: hpMN, - }, -]; - -/** - * Registers a single study hanging protocol which can be referenced as - * `@ohif/hp-exgtension.mn`, that has initial layouts which show images - * only display sets, up to a 2x2 view. - */ -export default function getHangingProtocolModule() { - return hangingProtocols; -} diff --git a/extensions/test-extension/src/index.tsx b/extensions/test-extension/src/index.tsx index 589d87ca5..16fe5dd2b 100644 --- a/extensions/test-extension/src/index.tsx +++ b/extensions/test-extension/src/index.tsx @@ -2,14 +2,11 @@ import { Types } from '@ohif/core'; import { id } from './id'; -import getHangingProtocolModule from './hp'; import getCustomizationModule from './getCustomizationModule'; // import {setViewportZoomPan, storeViewportZoomPan } from './custom-viewport/setViewportZoomPan'; import sameAs from './custom-attribute/sameAs'; import numberOfDisplaySets from './custom-attribute/numberOfDisplaySets'; -import numberOfDisplaySetsWithImages from './custom-attribute/numberOfDisplaySetsWithImages'; import maxNumImageFrames from './custom-attribute/maxNumImageFrames'; -import seriesDescriptionsFromDisplaySets from './custom-attribute/seriesDescriptionsFromDisplaySets'; /** * The test extension provides additional behaviour for testing various @@ -31,21 +28,11 @@ const testExtension: Types.Extensions.Extension = { */ preRegistration: ({ servicesManager }: Types.Extensions.ExtensionParams) => { const { hangingProtocolService } = servicesManager.services; - hangingProtocolService.addCustomAttribute( - 'seriesDescriptions', - 'Series Descriptions', - seriesDescriptionsFromDisplaySets - ); hangingProtocolService.addCustomAttribute( 'numberOfDisplaySets', 'Number of displays sets', numberOfDisplaySets ); - hangingProtocolService.addCustomAttribute( - 'numberOfDisplaySetsWithImages', - 'Number of displays sets with images', - numberOfDisplaySetsWithImages - ); hangingProtocolService.addCustomAttribute( 'maxNumImageFrames', 'Maximum of number of image frames', @@ -58,9 +45,6 @@ const testExtension: Types.Extensions.Extension = { ); }, - /** Registers some additional hanging protocols. See hp/index.tsx for more details */ - getHangingProtocolModule, - /** Registers some customizations */ getCustomizationModule, }; diff --git a/modes/basic-test-mode/src/toolbarButtons.js b/modes/basic-test-mode/src/toolbarButtons.js index 2d0492f6d..506e6b652 100644 --- a/modes/basic-test-mode/src/toolbarButtons.js +++ b/modes/basic-test-mode/src/toolbarButtons.js @@ -357,7 +357,7 @@ const toolbarButtons = [ { commandName: 'setHangingProtocol', commandOptions: { - protocolId: '@ohif/hp-extension.mn', + protocolId: '@ohif/mnGrid', stageId: '2x2', }, context: 'DEFAULT', @@ -372,7 +372,7 @@ const toolbarButtons = [ { commandName: 'setHangingProtocol', commandOptions: { - protocolId: '@ohif/hp-extension.mn', + protocolId: '@ohif/mnGrid', stageId: '3x1', }, context: 'DEFAULT', @@ -387,7 +387,7 @@ const toolbarButtons = [ { commandName: 'setHangingProtocol', commandOptions: { - protocolId: '@ohif/hp-extension.mn', + protocolId: '@ohif/mnGrid', stageId: '2x1', }, context: 'DEFAULT', @@ -402,7 +402,7 @@ const toolbarButtons = [ { commandName: 'setHangingProtocol', commandOptions: { - protocolId: '@ohif/hp-extension.mn', + protocolId: '@ohif/mnGrid', stageId: '1x1', }, context: 'DEFAULT', diff --git a/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts b/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts index 4ae568c2a..a0a16fbc5 100644 --- a/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts +++ b/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts @@ -9,7 +9,9 @@ import * as HangingProtocol from '../../types/HangingProtocol'; import { isDisplaySetFromUrl, sopInstanceLocation, -} from './isDisplaySetFromUrl'; +} from './custom-attribute/isDisplaySetFromUrl'; +import numberOfDisplaySetsWithImages from './custom-attribute/numberOfDisplaySetsWithImages'; +import seriesDescriptionsFromDisplaySets from './custom-attribute/seriesDescriptionsFromDisplaySets'; type Protocol = HangingProtocol.Protocol | HangingProtocol.ProtocolGenerator; @@ -93,6 +95,16 @@ export default class HangingProtocolService extends PubSubService { name: 'Gets the position of the specified sop instance', callback: sopInstanceLocation, }, + seriesDescriptions: { + name: 'seriesDescriptions', + description: 'List of Series Descriptions', + callback: seriesDescriptionsFromDisplaySets, + }, + numberOfDisplaySetsWithImages: { + name: 'numberOfDisplaySetsWithImages', + desription: 'Number of displays sets with images', + numberOfDisplaySetsWithImages, + }, }; listeners = {}; registeredImageLoadStrategies = {}; diff --git a/platform/core/src/services/HangingProtocolService/isDisplaySetFromUrl.ts b/platform/core/src/services/HangingProtocolService/custom-attribute/isDisplaySetFromUrl.ts similarity index 94% rename from platform/core/src/services/HangingProtocolService/isDisplaySetFromUrl.ts rename to platform/core/src/services/HangingProtocolService/custom-attribute/isDisplaySetFromUrl.ts index a271d5ecd..d1626919d 100644 --- a/platform/core/src/services/HangingProtocolService/isDisplaySetFromUrl.ts +++ b/platform/core/src/services/HangingProtocolService/custom-attribute/isDisplaySetFromUrl.ts @@ -1,4 +1,4 @@ -import { getSplitParam } from '../../utils'; +import { getSplitParam } from '../../../utils'; /** Indicates if the given display set is the one specified in the * displaySet parameter in the URL @@ -31,7 +31,7 @@ const isDisplaySetFromUrl = (displaySet): boolean => { * Returns undefined to fallback to the defaultValue */ function sopInstanceLocation(displaySets) { - const displaySet = displaySets[0]; + const displaySet = displaySets?.[0]; if (!displaySet) return; const initialSOPInstanceUID = getSplitParam('initialsopinstanceuid'); if (!initialSOPInstanceUID) return; diff --git a/extensions/test-extension/src/custom-attribute/numberOfDisplaySetsWithImages.ts b/platform/core/src/services/HangingProtocolService/custom-attribute/numberOfDisplaySetsWithImages.ts similarity index 100% rename from extensions/test-extension/src/custom-attribute/numberOfDisplaySetsWithImages.ts rename to platform/core/src/services/HangingProtocolService/custom-attribute/numberOfDisplaySetsWithImages.ts diff --git a/extensions/test-extension/src/custom-attribute/seriesDescriptionsFromDisplaySets.ts b/platform/core/src/services/HangingProtocolService/custom-attribute/seriesDescriptionsFromDisplaySets.ts similarity index 100% rename from extensions/test-extension/src/custom-attribute/seriesDescriptionsFromDisplaySets.ts rename to platform/core/src/services/HangingProtocolService/custom-attribute/seriesDescriptionsFromDisplaySets.ts diff --git a/platform/viewer/cypress/integration/customization/HangingProtocol.spec.js b/platform/viewer/cypress/integration/customization/HangingProtocol.spec.js index 6d3f87384..e57fd7d03 100644 --- a/platform/viewer/cypress/integration/customization/HangingProtocol.spec.js +++ b/platform/viewer/cypress/integration/customization/HangingProtocol.spec.js @@ -2,7 +2,7 @@ describe('OHIF HP', () => { const beforeSetup = () => { cy.checkStudyRouteInViewer( '1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1', - '&hangingProtocolId=@ohif/hp-extension.mn' + '&hangingProtocolId=@ohif/mnGrid' ); cy.expectMinimumThumbnails(3); cy.initCornerstoneToolsAliases(); diff --git a/platform/viewer/cypress/integration/customization/OHIFDoubleClick.spec.js b/platform/viewer/cypress/integration/customization/OHIFDoubleClick.spec.js index d60c1be91..7b46387fa 100644 --- a/platform/viewer/cypress/integration/customization/OHIFDoubleClick.spec.js +++ b/platform/viewer/cypress/integration/customization/OHIFDoubleClick.spec.js @@ -2,7 +2,7 @@ describe('OHIF Double Click', () => { beforeEach(() => { cy.checkStudyRouteInViewer( '1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1', - '&hangingProtocolId=@ohif/hp-extension.mn' + '&hangingProtocolId=@ohif/mnGrid' ); cy.expectMinimumThumbnails(3); cy.initCornerstoneToolsAliases(); diff --git a/platform/viewer/public/config/e2e.js b/platform/viewer/public/config/e2e.js index 3ec6fa559..0decbb941 100644 --- a/platform/viewer/public/config/e2e.js +++ b/platform/viewer/public/config/e2e.js @@ -14,7 +14,7 @@ window.config = { { friendlyName: 'StaticWado test data', namespace: '@ohif/extension-default.dataSourcesModule.dicomweb', - sourceName: 'dicomweb', + sourceName: 'e2e', configuration: { // The most important field to set for static WADO staticWado: true, @@ -32,6 +32,51 @@ window.config = { singlepart: 'video,thumbnail,pdf', }, }, + { + friendlyName: 'Static WADO Local Data', + namespace: '@ohif/extension-default.dataSourcesModule.dicomweb', + sourceName: 'local', + configuration: { + name: 'DCM4CHEE', + qidoRoot: '/dicomweb', + wadoRoot: '/dicomweb', + qidoSupportsIncludeField: false, + supportsReject: true, + supportsStow: true, + imageRendering: 'wadors', + thumbnailRendering: 'wadors', + enableStudyLazyLoad: true, + supportsFuzzyMatching: false, + supportsWildcard: true, + staticWado: true, + singlepart: 'bulkdata,video,pdf', + }, + }, + { + friendlyName: 'dcmjs DICOMWeb Server', + namespace: '@ohif/extension-default.dataSourcesModule.dicomweb', + sourceName: 'ohif', + configuration: { + name: 'aws', + // old server + // 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', + thumbnailRendering: 'wadors', + enableStudyLazyLoad: true, + supportsFuzzyMatching: false, + supportsWildcard: true, + staticWado: true, + singlepart: 'bulkdata,video,pdf', + }, + }, // { // friendlyName: 'StaticWado default data', // namespace: '@ohif/extension-default.dataSourcesModule.dicomweb', @@ -92,93 +137,6 @@ window.config = { // )) // }, // }, - defaultDataSourceName: 'dicomweb', - hotkeys: [ - { - commandName: 'incrementActiveViewport', - label: 'Next Viewport', - keys: ['right'], - }, - { - commandName: 'decrementActiveViewport', - label: 'Previous Viewport', - keys: ['left'], - }, - { commandName: 'rotateViewportCW', label: 'Rotate Right', keys: ['r'] }, - { commandName: 'rotateViewportCCW', label: 'Rotate Left', keys: ['l'] }, - { commandName: 'invertViewport', label: 'Invert', keys: ['i'] }, - { - commandName: 'flipViewportHorizontal', - label: 'Flip Horizontally', - keys: ['h'], - }, - { - commandName: 'flipViewportVertical', - label: 'Flip Vertically', - keys: ['v'], - }, - { commandName: 'scaleUpViewport', label: 'Zoom In', keys: ['+'] }, - { commandName: 'scaleDownViewport', label: 'Zoom Out', keys: ['-'] }, - { commandName: 'fitViewportToWindow', label: 'Zoom to Fit', keys: ['='] }, - { commandName: 'resetViewport', label: 'Reset', keys: ['space'] }, - { commandName: 'nextImage', label: 'Next Image', keys: ['down'] }, - { commandName: 'previousImage', label: 'Previous Image', keys: ['up'] }, - // { - // commandName: 'previousViewportDisplaySet', - // label: 'Previous Series', - // keys: ['pagedown'], - // }, - // { - // commandName: 'nextViewportDisplaySet', - // label: 'Next Series', - // keys: ['pageup'], - // }, - { commandName: 'setZoomTool', label: 'Zoom', keys: ['z'] }, - // ~ Window level presets - { - commandName: 'windowLevelPreset1', - label: 'W/L Preset 1', - keys: ['1'], - }, - { - commandName: 'windowLevelPreset2', - label: 'W/L Preset 2', - keys: ['2'], - }, - { - commandName: 'windowLevelPreset3', - label: 'W/L Preset 3', - keys: ['3'], - }, - { - commandName: 'windowLevelPreset4', - label: 'W/L Preset 4', - keys: ['4'], - }, - { - commandName: 'windowLevelPreset5', - label: 'W/L Preset 5', - keys: ['5'], - }, - { - commandName: 'windowLevelPreset6', - label: 'W/L Preset 6', - keys: ['6'], - }, - { - commandName: 'windowLevelPreset7', - label: 'W/L Preset 7', - keys: ['7'], - }, - { - commandName: 'windowLevelPreset8', - label: 'W/L Preset 8', - keys: ['8'], - }, - { - commandName: 'windowLevelPreset9', - label: 'W/L Preset 9', - keys: ['9'], - }, - ], + defaultDataSourceName: 'e2e', + hotkeys: [], }; From dc61d8723824365d4cf02d1a948fca8a45acdbaf Mon Sep 17 00:00:00 2001 From: Leonardo Campos Date: Thu, 20 Apr 2023 13:39:37 -0300 Subject: [PATCH 12/54] chore(version): updated Orthanc from 1.5.7 to 1.11.0 (#3330) --- .docker/Nginx-Orthanc/docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.docker/Nginx-Orthanc/docker-compose.yml b/.docker/Nginx-Orthanc/docker-compose.yml index b12382f39..eba7911a3 100644 --- a/.docker/Nginx-Orthanc/docker-compose.yml +++ b/.docker/Nginx-Orthanc/docker-compose.yml @@ -2,7 +2,7 @@ version: '3.5' services: orthanc: - image: jodogne/orthanc-plugins:1.5.7 + image: jodogne/orthanc-plugins:1.11.0 hostname: orthanc volumes: # Config From 69d8e6a1916970359a9766c99a3ae9fcb1bc0ce4 Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Tue, 25 Apr 2023 17:25:10 -0400 Subject: [PATCH 13/54] fix(SR): When loading DICOM SR, only one measurement is shown with no way to show others (#3228) * fix: Make the cornerstone sR viewport show all measurements * PR fixes * PR fixes * Add a DICOM SR hanging protocol * Duplicate the hanging protocol for seg as well * PR requested change * PR requested changes * PR fixes plus merge update fixes * PR fixes and integration test fix * PR - documentation --- .../src/getSopClassHandlerModule.js | 1 + .../cornerstone-dicom-seg/src/index.tsx | 9 +- extensions/cornerstone-dicom-sr/package.json | 4 +- .../src/commandsModule.js | 21 +- .../src/getSopClassHandlerModule.ts | 108 ++++--- extensions/cornerstone-dicom-sr/src/index.tsx | 5 +- .../cornerstone-dicom-sr/src/onModeEnter.js | 2 +- .../utils/createReferencedImageDisplaySet.ts | 89 ++++++ .../viewports/OHIFCornerstoneSRViewport.tsx | 30 +- extensions/cornerstone/package.json | 4 +- .../src/Viewport/OHIFCornerstoneViewport.tsx | 3 +- extensions/cornerstone/src/index.tsx | 2 +- .../CornerstoneCacheService.ts | 20 +- .../src/services/ViewportService/Viewport.ts | 7 +- .../utils/findSRWithSameSeriesDescription.ts | 2 +- .../dicom-pdf/src/getSopClassHandlerModule.js | 2 +- .../src/getSopClassHandlerModule.js | 2 +- extensions/measurement-tracking/package.json | 4 +- platform/core/src/classes/MetadataProvider.js | 1 + .../DisplaySetService/DisplaySetService.ts | 286 ++++++++++++------ .../HangingProtocolService/HPMatcher.js | 2 +- platform/core/src/types/index.ts | 3 +- .../OHIFMeasurementPanel.spec.js | 4 +- yarn.lock | 18 +- 24 files changed, 457 insertions(+), 172 deletions(-) create mode 100644 extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts diff --git a/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js b/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js index 774294332..de9212d84 100644 --- a/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js +++ b/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js @@ -53,6 +53,7 @@ function _getDisplaySetsFromSeries( segments: {}, sopClassUids, instance, + instances: [instance], wadoRoot, wadoUriRoot, wadoUri, diff --git a/extensions/cornerstone-dicom-seg/src/index.tsx b/extensions/cornerstone-dicom-seg/src/index.tsx index b77fb6677..22a6ec491 100644 --- a/extensions/cornerstone-dicom-seg/src/index.tsx +++ b/extensions/cornerstone-dicom-seg/src/index.tsx @@ -3,7 +3,7 @@ import React from 'react'; import { Types } from '@ohif/core'; -import getSopClassHandlerModule from './getSopClassHandlerModule'; +import getSopClassHandlerModule, { protocols } from './getSopClassHandlerModule'; import PanelSegmentation from './panels/PanelSegmentation'; import getHangingProtocolModule from './getHangingProtocolModule'; @@ -37,7 +37,7 @@ const extension = { * iconName, iconLabel, label, component} object. Example of a panel module * is the StudyBrowserPanel that is provided by the default extension in OHIF. */ - getPanelModule: ({ servicesManager, commandsManager, extensionManager }): Types.Panel[] => { + getPanelModule: ({ servicesManager, commandsManager, extensionManager }: Types.Extensions.ExtensionParams): Types.Panel[] => { const wrappedPanelSegmentation = () => { return ( { return ( @@ -85,3 +86,7 @@ const extension = { }; export default extension; + +// Export the protocols separately to allow for extending it at compile time +// in other modules +export { protocols }; diff --git a/extensions/cornerstone-dicom-sr/package.json b/extensions/cornerstone-dicom-sr/package.json index a566c0c0d..2dc6b9edc 100644 --- a/extensions/cornerstone-dicom-sr/package.json +++ b/extensions/cornerstone-dicom-sr/package.json @@ -46,7 +46,7 @@ "@babel/runtime": "^7.20.13", "classnames": "^2.3.2", "@cornerstonejs/adapters": "^0.6.0", - "@cornerstonejs/core": "^0.40.0", - "@cornerstonejs/tools": "^0.60.1" + "@cornerstonejs/core": "^0.42.2", + "@cornerstonejs/tools": "^0.61.11" } } diff --git a/extensions/cornerstone-dicom-sr/src/commandsModule.js b/extensions/cornerstone-dicom-sr/src/commandsModule.js index 7b685ed44..f8c9459e4 100644 --- a/extensions/cornerstone-dicom-sr/src/commandsModule.js +++ b/extensions/cornerstone-dicom-sr/src/commandsModule.js @@ -1,6 +1,6 @@ import { metaData, utilities } from '@cornerstonejs/core'; -import OHIF from '@ohif/core'; +import OHIF, { DicomMetadataStore } from '@ohif/core'; import dcmjs from 'dcmjs'; import { adaptersSR } from '@cornerstonejs/adapters'; @@ -41,7 +41,6 @@ const _generateReport = ( if (typeof dataset.SpecificCharacterSet === 'undefined') { dataset.SpecificCharacterSet = 'ISO_IR 192'; } - return dataset; }; @@ -104,7 +103,18 @@ const commandsModule = ({}) => { additionalFindingTypes, options ); - const { StudyInstanceUID } = naturalizedReport; + + const { StudyInstanceUID, ContentSequence } = naturalizedReport; + // The content sequence has 5 or more elements, of which + // the `[4]` element contains the annotation data, so this is + // checking that there is some annotation data present. + if (!ContentSequence?.[4].ContentSequence?.length) { + console.log( + 'naturalizedReport missing imaging content', + naturalizedReport + ); + throw new Error('Invalid report, no content'); + } await dataSource.store.dicom(naturalizedReport); @@ -112,6 +122,11 @@ const commandsModule = ({}) => { dataSource.deleteStudyMetadataPromise(StudyInstanceUID); } + // The "Mode" route listens for DicomMetadataStore changes + // When a new instance is added, it listens and + // automatically calls makeDisplaySets + DicomMetadataStore.addInstances([naturalizedReport], true); + return naturalizedReport; } catch (error) { console.warn(error); diff --git a/extensions/cornerstone-dicom-sr/src/getSopClassHandlerModule.ts b/extensions/cornerstone-dicom-sr/src/getSopClassHandlerModule.ts index 54a810a8d..a52234182 100644 --- a/extensions/cornerstone-dicom-sr/src/getSopClassHandlerModule.ts +++ b/extensions/cornerstone-dicom-sr/src/getSopClassHandlerModule.ts @@ -1,12 +1,15 @@ import { SOPClassHandlerName, SOPClassHandlerId } from './id'; -import { utils, classes } from '@ohif/core'; +import { utils, classes, DisplaySetService, Types } from '@ohif/core'; import addMeasurement from './utils/addMeasurement'; import isRehydratable from './utils/isRehydratable'; import { adaptersSR } from '@cornerstonejs/adapters'; +type InstanceMetadata = Types.InstanceMetadata; + const { CodeScheme: Cornerstone3DCodeScheme } = adaptersSR.Cornerstone3D; const { ImageSet, MetadataProvider: metadataProvider } = classes; + // TODO -> // Add SR thumbnail // Make viewport @@ -22,6 +25,17 @@ const sopClassUids = [ const CORNERSTONE_3D_TOOLS_SOURCE_NAME = 'Cornerstone3DTools'; const CORNERSTONE_3D_TOOLS_SOURCE_VERSION = '0.1'; +const validateSameStudyUID = (uid: string, instances): void => { + instances.forEach(it => { + if (it.StudyInstanceUID !== uid) { + console.warn('Not all instances have the same UID', uid, it); + throw new Error( + `Instances ${it.SOPInstanceUID} does not belong to ${uid}` + ); + } + }); +}; + const CodeNameCodeSequenceValues = { ImagingMeasurementReport: '126000', ImageLibrary: '111028', @@ -50,15 +64,38 @@ const RELATIONSHIP_TYPE = { const CORNERSTONE_FREETEXT_CODE_VALUE = 'CORNERSTONEFREETEXT'; +/** + * Adds instances to the DICOM SR series, rather than creating a new + * series, so that as SR's are saved, they append to the series, and the + * key image display set gets updated as well, containing just the new series. + * @param instances is a list of instances from THIS series that are not + * in this DICOM SR Display Set already. + */ +function addInstances( + instances: InstanceMetadata[], + displaySetService: DisplaySetService +) { + this.instances.push(...instances); + utils.sortStudyInstances(this.instances); + // The last instance is the newest one, so is the one most interesting. + // Eventually, the SR viewer should have the ability to choose which SR + // gets loaded, and to navigate among them. + this.instance = this.instances[this.instances.length - 1]; + this.isLoaded = false; + if (this.keyImageDisplaySet) { + this.load(); + this.keyImageDisplaySet.updateInstances(); + displaySetService.setDisplaySetMetadataInvalidated( + this.keyImageDisplaySet.displaySetInstanceUID + ); + } + return this; +} + /** * DICOM SR SOP Class Handler * For all referenced images in the TID 1500/300 sections, add an image to the - * display (this is TODO - it is not the actual behaviour below unfortunately) - * - * This will only display and rehydrate the latest DICOM SR in the given series - * It would be possible to add the ability to view older series rehydrations - * in the future. - * + * display. * @param instances is a set of instances all from the same series * @param servicesManager is the services that can be used for creating * @returns The list of display sets created for the given instances object @@ -74,6 +111,9 @@ function _getDisplaySetsFromSeries( } utils.sortStudyInstances(instances); + // The last instance is the newest one, so is the one most interesting. + // Eventually, the SR viewer should have the ability to choose which SR + // gets loaded, and to navigate among them. const instance = instances[instances.length - 1]; const { @@ -86,11 +126,12 @@ function _getDisplaySetsFromSeries( ConceptNameCodeSequence, SOPClassUID, } = instance; + validateSameStudyUID(instance.StudyInstanceUID, instances); if ( !ConceptNameCodeSequence || ConceptNameCodeSequence.CodeValue !== - CodeNameCodeSequenceValues.ImagingMeasurementReport + CodeNameCodeSequenceValues.ImagingMeasurementReport ) { console.log( 'Only support Imaging Measurement Report SRs (TID1500) for this renderer.' @@ -111,14 +152,13 @@ function _getDisplaySetsFromSeries( SOPClassHandlerId, SOPClassUID, instances, - // Others is a historical value used for instances which is deprecated and will be removed - others: instances, referencedImages: null, measurements: null, isDerivedDisplaySet: true, isLoaded: false, sopClassUids, instance, + addInstances, }; displaySet.load = () => _load(displaySet, servicesManager, extensionManager); @@ -327,7 +367,7 @@ function _getMeasurements(ImagingMeasurementReportContentSequence) { trackingUniqueIdentifier => { const mergedContentSequence = mergedContentSequencesByTrackingUniqueIdentifiers[ - trackingUniqueIdentifier + trackingUniqueIdentifier ]; const measurement = _processMeasurement(mergedContentSequence); @@ -367,7 +407,7 @@ function _getMergedContentSequencesByTrackingUniqueIdentifiers( if ( mergedContentSequencesByTrackingUniqueIdentifiers[ - trackingUniqueIdentifier + trackingUniqueIdentifier ] === undefined ) { // Add the full ContentSequence @@ -473,18 +513,18 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) { CodeNameCodeSequenceValues.TrackingIdentifier ); - const Finding = mergedContentSequence.find( + const finding = mergedContentSequence.find( item => item.ConceptNameCodeSequence.CodeValue === CodeNameCodeSequenceValues.Finding ); - const FindingSites = mergedContentSequence.filter( + const findingSites = mergedContentSequence.filter( item => item.ConceptNameCodeSequence.CodingSchemeDesignator === - CodingSchemeDesignators.SRT && + CodingSchemeDesignators.SRT && item.ConceptNameCodeSequence.CodeValue === - CodeNameCodeSequenceValues.FindingSite + CodeNameCodeSequenceValues.FindingSite ); const measurement = { @@ -496,28 +536,28 @@ function _processNonGeometricallyDefinedMeasurement(mergedContentSequence) { }; if ( - Finding && + finding && CodingSchemeDesignators.CornerstoneCodeSchemes.includes( - Finding.ConceptCodeSequence.CodingSchemeDesignator + finding.ConceptCodeSequence.CodingSchemeDesignator ) && - Finding.ConceptCodeSequence.CodeValue === - CodeNameCodeSequenceValues.CornerstoneFreeText + finding.ConceptCodeSequence.CodeValue === + CodeNameCodeSequenceValues.CornerstoneFreeText ) { measurement.labels.push({ label: CORNERSTONE_FREETEXT_CODE_VALUE, - value: Finding.ConceptCodeSequence.CodeMeaning, + value: finding.ConceptCodeSequence.CodeMeaning, }); } // TODO -> Eventually hopefully support SNOMED or some proper code library, just free text for now. - if (FindingSites.length) { - const cornerstoneFreeTextFindingSite = FindingSites.find( + if (findingSites.length) { + const cornerstoneFreeTextFindingSite = findingSites.find( FindingSite => CodingSchemeDesignators.CornerstoneCodeSchemes.includes( FindingSite.ConceptCodeSequence.CodingSchemeDesignator ) && FindingSite.ConceptCodeSequence.CodeValue === - CodeNameCodeSequenceValues.CornerstoneFreeText + CodeNameCodeSequenceValues.CornerstoneFreeText ); if (cornerstoneFreeTextFindingSite) { @@ -633,17 +673,16 @@ function _getReferencedImagesList(ImagingMeasurementReportContentSequence) { _getSequenceAsArray(ImageLibraryGroup.ContentSequence).forEach(item => { const { ReferencedSOPSequence } = item; + if (!ReferencedSOPSequence) return; + for (const ref of _getSequenceAsArray(ReferencedSOPSequence)) { + if (ref.ReferencedSOPClassUID) { + const { ReferencedSOPClassUID, ReferencedSOPInstanceUID } = ref; - if (item.hasOwnProperty('ReferencedSOPClassUID')) { - const { - ReferencedSOPClassUID, - ReferencedSOPInstanceUID, - } = ReferencedSOPSequence; - - referencedImages.push({ - ReferencedSOPClassUID, - ReferencedSOPInstanceUID, - }); + referencedImages.push({ + ReferencedSOPClassUID, + ReferencedSOPInstanceUID, + }); + } } }); @@ -651,6 +690,7 @@ function _getReferencedImagesList(ImagingMeasurementReportContentSequence) { } function _getSequenceAsArray(sequence) { + if (!sequence) return []; return Array.isArray(sequence) ? sequence : [sequence]; } diff --git a/extensions/cornerstone-dicom-sr/src/index.tsx b/extensions/cornerstone-dicom-sr/src/index.tsx index 53d1217e7..9b87ea98c 100644 --- a/extensions/cornerstone-dicom-sr/src/index.tsx +++ b/extensions/cornerstone-dicom-sr/src/index.tsx @@ -9,6 +9,7 @@ import preRegistration from './init'; import { id } from './id.js'; import toolNames from './tools/toolNames'; import hydrateStructuredReport from './utils/hydrateStructuredReport'; +import createReferencedImageDisplaySet from './utils/createReferencedImageDisplaySet'; const Component = React.lazy(() => { return import( @@ -57,8 +58,6 @@ const dicomSRExtension = { }, getCommandsModule, getSopClassHandlerModule, - getHangingProtocolModule, - // Include dynmically computed values such as toolNames not known till instantiation getUtilityModule({ servicesManager }) { return [ @@ -75,4 +74,4 @@ const dicomSRExtension = { export default dicomSRExtension; // Put static exports here so they can be type checked -export { hydrateStructuredReport, srProtocol }; +export { hydrateStructuredReport, createReferencedImageDisplaySet, srProtocol }; diff --git a/extensions/cornerstone-dicom-sr/src/onModeEnter.js b/extensions/cornerstone-dicom-sr/src/onModeEnter.js index 61b6985ef..fc4b1efce 100644 --- a/extensions/cornerstone-dicom-sr/src/onModeEnter.js +++ b/extensions/cornerstone-dicom-sr/src/onModeEnter.js @@ -4,7 +4,7 @@ export default function onModeEnter({ servicesManager }) { const { displaySetService } = servicesManager.services; const displaySetCache = displaySetService.getDisplaySetCache(); - const srDisplaySets = displaySetCache.filter( + const srDisplaySets = [...displaySetCache.values()].filter( ds => ds.SOPClassHandlerId === SOPClassHandlerId ); diff --git a/extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts b/extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts new file mode 100644 index 000000000..0abff2b3c --- /dev/null +++ b/extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts @@ -0,0 +1,89 @@ +import { DisplaySetService, classes } from '@ohif/core'; + +const ImageSet = classes.ImageSet; + +const findInstance = (measurement, displaySetService: DisplaySetService) => { + const { + displaySetInstanceUID, + ReferencedSOPInstanceUID: sopUid, + } = measurement; + const referencedDisplaySet = displaySetService.getDisplaySetByUID( + displaySetInstanceUID + ); + if (!referencedDisplaySet.images) return; + return referencedDisplaySet.images.find(it => it.SOPInstanceUID === sopUid); +}; + +/** Finds references to display sets inside the measurements + * contained within the provided display set. + * @return an array of instances referenced. + */ +const findReferencedInstances = ( + displaySetService: DisplaySetService, + displaySet +) => { + const instances = []; + const instanceById = {}; + for (const measurement of displaySet.measurements) { + const { imageId } = measurement; + if (!imageId) continue; + if (instanceById[imageId]) continue; + + const instance = findInstance(measurement, displaySetService); + if (!instance) { + console.log('Measurement', measurement, 'had no instances found'); + continue; + } + + instanceById[imageId] = instance; + instances.push(instance); + } + return instances; +}; + +/** + * Creates a new display set containing a single image instance for each + * referenced image. + * + * @param displaySetService + * @param displaySet - containing measurements referencing images. + * @returns A new (registered/active) display set containing the referenced images + */ +const createReferencedImageDisplaySet = (displaySetService, displaySet) => { + const instances = findReferencedInstances(displaySetService, displaySet); + // This will be a member function of the created image set + const updateInstances = function() { + this.images.splice( + 0, + this.images.length, + ...findReferencedInstances(displaySetService, displaySet) + ); + this.numImageFrames = this.images.length; + }; + + const imageSet = new ImageSet(instances); + const instance = instances[0]; + imageSet.setAttributes({ + displaySetInstanceUID: imageSet.uid, // create a local alias for the imageSet UID + SeriesDate: instance.SeriesDate, + SeriesTime: instance.SeriesTime, + SeriesInstanceUID: imageSet.uid, + StudyInstanceUID: instance.StudyInstanceUID, + SeriesNumber: instance.SeriesNumber || 0, + SOPClassUID: instance.SOPClassUID, + SeriesDescription: `${displaySet.SeriesDescription} KO ${displaySet.instance.SeriesNumber}`, + Modality: 'KO', + isMultiFrame: false, + numImageFrames: instances.length, + SOPClassHandlerId: `@ohif/extension-default.sopClassHandlerModule.stack`, + isReconstructable: false, + madeInClient: true, + updateInstances, + }); + + displaySetService.addDisplaySets(imageSet); + + return imageSet; +}; + +export default createReferencedImageDisplaySet; diff --git a/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx b/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx index c3db19b8c..75b34893f 100644 --- a/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx +++ b/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx @@ -15,6 +15,7 @@ import { ViewportActionBar, } from '@ohif/ui'; import hydrateStructuredReport from '../utils/hydrateStructuredReport'; +import createReferencedImageDisplaySet from '../utils/createReferencedImageDisplaySet'; const { formatDate } = utils; @@ -59,7 +60,6 @@ function OHIFCornerstoneSRViewport(props) { referencedDisplaySetMetadata, setReferencedDisplaySetMetadata, ] = useState(null); - const [isHydrated, setIsHydrated] = useState(srDisplaySet.isHydrated); const [element, setElement] = useState(null); const { viewports, activeViewportIndex } = viewportGrid; @@ -89,9 +89,9 @@ function OHIFCornerstoneSRViewport(props) { { servicesManager, extensionManager }, displaySetInstanceUID ); - const displaySets = displaySetService.getDisplaySetsForSeries( - SeriesInstanceUIDs[0] - ); + const displaySets = srDisplaySet.keyImageDisplaySet + ? [srDisplaySet.keyImageDisplaySet] + : displaySetService.getDisplaySetsForSeries(SeriesInstanceUIDs[0]); if (displaySets.length) { viewportGridService.setDisplaySetsForViewports([ { @@ -293,8 +293,6 @@ function OHIFCornerstoneSRViewport(props) { if (!srDisplaySet.isLoaded) { srDisplaySet.load(); } - setIsHydrated(srDisplaySet.isHydrated); - const numMeasurements = srDisplaySet.measurements.length; setMeasurementCount(numMeasurements); }, [srDisplaySet]); @@ -382,6 +380,7 @@ function OHIFCornerstoneSRViewport(props) { label: viewportLabel, useAltStyling: true, studyDate: formatDate(StudyDate), + currentSeries: SeriesNumber, seriesDescription: SeriesDescription || '', patientInformation: { patientName: PatientName @@ -424,6 +423,7 @@ OHIFCornerstoneSRViewport.propTypes = { viewportIndex: PropTypes.number.isRequired, dataSource: PropTypes.object, children: PropTypes.node, + viewportLabel: PropTypes.string, customProps: PropTypes.object, viewportOptions: PropTypes.object, viewportLabel: PropTypes.string, @@ -440,14 +440,18 @@ async function _getViewportReferencedDisplaySetData( measurementSelected, displaySetService ) { - const { measurements } = displaySet; - const measurement = measurements[measurementSelected]; + if (!displaySet.keyImageDisplaySet) { + // Create a new display set, and preserve a reference to it here, + // so that it can be re-displayed and shown inside the SR viewport. + // This is only for ease of redisplay - the display set is stored in the + // usual manner in the display set service. + displaySet.keyImageDisplaySet = createReferencedImageDisplaySet( + displaySetService, + displaySet + ); + } - const { displaySetInstanceUID } = measurement; - - const referencedDisplaySet = displaySetService.getDisplaySetByUID( - displaySetInstanceUID - ); + const referencedDisplaySet = displaySet.keyImageDisplaySet; const image0 = referencedDisplaySet.images[0]; const referencedDisplaySetMetadata = { diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json index 55a5b76d9..526074be1 100644 --- a/extensions/cornerstone/package.json +++ b/extensions/cornerstone/package.json @@ -49,9 +49,9 @@ "dependencies": { "@babel/runtime": "^7.20.13", "@cornerstonejs/adapters": "^0.6.0", - "@cornerstonejs/core": "^0.40.0", + "@cornerstonejs/core": "^0.42.2", "@cornerstonejs/streaming-image-volume-loader": "^0.16.0", - "@cornerstonejs/tools": "^0.60.1", + "@cornerstonejs/tools": "^0.61.11", "@kitware/vtk.js": "26.5.6", "html2canvas": "^1.4.1", "lodash.debounce": "4.0.8", diff --git a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx index 0a9d8ac89..f3e061900 100644 --- a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx +++ b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx @@ -550,6 +550,7 @@ function _checkForCachedJumpToMeasurementEvents( const displaysUIDs = displaySets.map( displaySet => displaySet.displaySetInstanceUID ); + if (!displaysUIDs?.length) return; const measurementIdToJumpTo = measurementService.getJumpToMeasurement( viewportIndex @@ -561,7 +562,7 @@ function _checkForCachedJumpToMeasurementEvents( measurementIdToJumpTo ); - if (displaysUIDs.includes(measurement.displaySetInstanceUID)) { + if (displaysUIDs.includes(measurement?.displaySetInstanceUID)) { _jumpToMeasurement( measurement, elementRef, diff --git a/extensions/cornerstone/src/index.tsx b/extensions/cornerstone/src/index.tsx index 165d70cd9..29387df19 100644 --- a/extensions/cornerstone/src/index.tsx +++ b/extensions/cornerstone/src/index.tsx @@ -93,7 +93,7 @@ const cornerstoneExtension: Types.Extensions.Extension = { return ( diff --git a/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts b/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts index 7eb2d6751..447dfd654 100644 --- a/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts +++ b/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts @@ -1,5 +1,10 @@ import { ServicesManager, Types } from '@ohif/core'; -import { cache as cs3DCache, Enums, volumeLoader } from '@cornerstonejs/core'; +import { + cache as cs3DCache, + Enums, + volumeLoader, + utilities as utils, +} from '@cornerstonejs/core'; import getCornerstoneViewportType from '../../utils/getCornerstoneViewportType'; import { @@ -11,14 +16,14 @@ const VOLUME_LOADER_SCHEME = 'cornerstoneStreamingImageVolume'; class CornerstoneCacheService { static REGISTRATION = { - name: 'cornerstoneCacheService', - altName: 'CornerstoneCacheService', + name: 'cornerstoneCacheService', + altName: 'CornerstoneCacheService', create: ({ servicesManager, }: Types.Extensions.ExtensionParams): CornerstoneCacheService => { return new CornerstoneCacheService(servicesManager); - }, - }; + }, + }; stackImageIds: Map = new Map(); volumeImageIds: Map = new Map(); @@ -91,7 +96,10 @@ class CornerstoneCacheService { displaySetService ) { if (viewportData.viewportType === Enums.ViewportType.STACK) { - throw new Error('Invalidation of StackViewport is not supported yet'); + return this._getCornerstoneStackImageIds( + displaySetService.getDisplaySetByUID(invalidatedDisplaySetInstanceUID), + dataSource + ); } // Todo: grab the volume and get the id from the viewport itself diff --git a/extensions/cornerstone/src/services/ViewportService/Viewport.ts b/extensions/cornerstone/src/services/ViewportService/Viewport.ts index 4f43aff23..c56af0836 100644 --- a/extensions/cornerstone/src/services/ViewportService/Viewport.ts +++ b/extensions/cornerstone/src/services/ViewportService/Viewport.ts @@ -203,6 +203,10 @@ class ViewportInfo { orientation = getCornerstoneOrientation(viewportOptionsEntry.orientation); } + if (!toolGroupId) { + toolGroupId = DEFAULT_TOOLGROUP_ID; + } + this.setViewportOptions({ ...viewportOptionsEntry, viewportId: this.viewportId, @@ -228,7 +232,8 @@ class ViewportInfo { } public getSyncGroups(): SyncGroup[] { - return this.viewportOptions.syncGroups || []; + this.viewportOptions.syncGroups ||= []; + return this.viewportOptions.syncGroups; } public getDisplaySetOptions(): Array { diff --git a/extensions/default/src/utils/findSRWithSameSeriesDescription.ts b/extensions/default/src/utils/findSRWithSameSeriesDescription.ts index 476343fb5..d50c76976 100644 --- a/extensions/default/src/utils/findSRWithSameSeriesDescription.ts +++ b/extensions/default/src/utils/findSRWithSameSeriesDescription.ts @@ -40,7 +40,7 @@ export default function findSRWithSameSeriesDescription( SeriesTime, SeriesNumber, Modality, - InstanceNumber: sameSeries.others.length + 1, + InstanceNumber: sameSeries.instances.length + 1, }; } diff --git a/extensions/dicom-pdf/src/getSopClassHandlerModule.js b/extensions/dicom-pdf/src/getSopClassHandlerModule.js index 949edfd42..99a9bae80 100644 --- a/extensions/dicom-pdf/src/getSopClassHandlerModule.js +++ b/extensions/dicom-pdf/src/getSopClassHandlerModule.js @@ -50,7 +50,7 @@ const _getDisplaySetsFromSeries = ( referencedImages: null, measurements: null, pdfUrl, - others: [instance], + instances: [instance], thumbnailSrc: dataSource.retrieve.directURL({ instance, defaultPath: '/thumbnail', diff --git a/extensions/dicom-video/src/getSopClassHandlerModule.js b/extensions/dicom-video/src/getSopClassHandlerModule.js index 31aebed9b..4be185e74 100644 --- a/extensions/dicom-video/src/getSopClassHandlerModule.js +++ b/extensions/dicom-video/src/getSopClassHandlerModule.js @@ -70,7 +70,7 @@ const _getDisplaySetsFromSeries = ( singlepart: 'video', tag: 'PixelData', }), - others: [instance], + instances: [instance], thumbnailSrc: dataSource.retrieve.directURL({ instance, defaultPath: '/thumbnail', diff --git a/extensions/measurement-tracking/package.json b/extensions/measurement-tracking/package.json index 59ab9e3b9..b07b17d2e 100644 --- a/extensions/measurement-tracking/package.json +++ b/extensions/measurement-tracking/package.json @@ -32,8 +32,8 @@ "peerDependencies": { "@ohif/core": "^3.0.0", "classnames": "^2.3.2", - "@cornerstonejs/core": "^0.40.0", - "@cornerstonejs/tools": "^0.60.1", + "@cornerstonejs/core": "^0.42.2", + "@cornerstonejs/tools": "^0.61.11", "@ohif/extension-cornerstone-dicom-sr": "^3.0.0", "dcmjs": "^0.29.5", "lodash.debounce": "^4.17.21", diff --git a/platform/core/src/classes/MetadataProvider.js b/platform/core/src/classes/MetadataProvider.js index 32f482e74..02bf2b4e8 100644 --- a/platform/core/src/classes/MetadataProvider.js +++ b/platform/core/src/classes/MetadataProvider.js @@ -441,6 +441,7 @@ class MetadataProvider { } getUIDsFromImageID(imageId) { + if (!imageId) throw new Error('MetadataProvider::Empty imageId'); // TODO: adding csiv here is not really correct. Probably need to use // metadataProvider.addImageIdToUIDs(imageId, { // StudyInstanceUID, diff --git a/platform/core/src/services/DisplaySetService/DisplaySetService.ts b/platform/core/src/services/DisplaySetService/DisplaySetService.ts index 552e7936c..b77322b2c 100644 --- a/platform/core/src/services/DisplaySetService/DisplaySetService.ts +++ b/platform/core/src/services/DisplaySetService/DisplaySetService.ts @@ -1,31 +1,40 @@ +import { InstanceMetadata } from '../../types'; import { PubSubService } from '../_shared/pubSubServiceInterface'; import EVENTS from './EVENTS'; -const displaySetCache = []; - -/** - * Find an instance in a list of instances, comparing by SOP instance UID - */ -const findInSet = (instance, list) => { - if (!list) return false; - for (const elem of list) { - if (!elem) continue; - if (elem === instance) return true; - if (elem.SOPInstanceUID === instance.SOPInstanceUID) return true; - } - return false; +export type DisplaySet = { + displaySetInstanceUID: string; + instances: InstanceMetadata[]; + StudyInstanceUID: string; + SeriesInstanceUID?: string; + numImages?: number; }; +const displaySetCache = new Map(); + /** - * Find an instance in a display set - * @returns true if found + * Filters the instances set by instances not in + * display sets. Done in O(n) time. */ -const findInstance = (instance, displaySets) => { - for (const displayset of displaySets) { - if (findInSet(instance, displayset.images)) return true; - if (findInSet(instance, displayset.others)) return true; - } - return false; +const filterInstances = ( + instances: InstanceMetadata[], + displaySets: DisplaySet[] +): InstanceMetadata[] => { + const dsInstancesSOP = new Set(); + displaySets.forEach(ds => { + const dsInstances = ds.instances; + if (!dsInstances) { + console.warn('No instances in', ds); + } else { + dsInstances.forEach(instance => + dsInstancesSOP.add(instance.SOPInstanceUID) + ); + } + }); + + return instances.filter( + instance => !dsInstancesSOP.has(instance.SOPInstanceUID) + ); }; export default class DisplaySetService extends PubSubService { @@ -38,6 +47,13 @@ export default class DisplaySetService extends PubSubService { }; public activeDisplaySets = []; + + protected activeDisplaySetsMap = new Map(); + + // Record if the active display sets changed - used to group change events so + // that fewer events need to be fired when creating multiple display sets + protected activeDisplaySetsChanged = false; + constructor() { super(EVENTS); } @@ -46,64 +62,85 @@ export default class DisplaySetService extends PubSubService { this.extensionManager = extensionManager; this.SOPClassHandlerIds = SOPClassHandlerIds; this.activeDisplaySets = []; + this.activeDisplaySetsMap.clear(); } - _addDisplaySetsToCache(displaySets) { + _addDisplaySetsToCache(displaySets: DisplaySet[]) { displaySets.forEach(displaySet => { - displaySetCache.push(displaySet); + displaySetCache.set(displaySet.displaySetInstanceUID, displaySet); }); } - _addActiveDisplaySets(displaySets) { - const activeDisplaySets = this.activeDisplaySets; + _addActiveDisplaySets(displaySets: DisplaySet[]) { + const { activeDisplaySets, activeDisplaySetsMap } = this; displaySets.forEach(displaySet => { - // This test makes adding display sets an N^2 operation, so it might - // become important to do this in an efficient manner for large - // numbers of display sets. - if (!activeDisplaySets.includes(displaySet)) { + if (!activeDisplaySetsMap.has(displaySet.displaySetInstanceUID)) { + this.activeDisplaySetsChanged = true; activeDisplaySets.push(displaySet); + activeDisplaySetsMap.set(displaySet.displayInstanceUID, displaySet); } }); } - getDisplaySetCache() { + /** + * Adds new display sets directly, as specified. + * Use this function when the display sets are created externally directly + * rather than using the default sop class handlers to create display sets. + */ + public addDisplaySets(...displaySets: DisplaySet[]): string[] { + this._addDisplaySetsToCache(displaySets); + this._addActiveDisplaySets(displaySets); + + // The activeDisplaySetsChanged flag is only seen if we add display sets + // so, don't broadcast the change if all the display sets were pre-existing. + this.activeDisplaySetsChanged = false; + this._broadcastEvent(EVENTS.DISPLAY_SETS_ADDED, { + displaySetsAdded: displaySets, + options: { madeInClient: displaySets[0].madeInClient }, + }); + return displaySets; + } + + public getDisplaySetCache(): Map { return displaySetCache; } - getMostRecentDisplaySet() { + public getMostRecentDisplaySet(): DisplaySet { return this.activeDisplaySets[this.activeDisplaySets.length - 1]; } - getActiveDisplaySets() { + public getActiveDisplaySets(): DisplaySet[] { return this.activeDisplaySets; } - getDisplaySetsForSeries = SeriesInstanceUID => { - return displaySetCache.filter( - displaySet => displaySet.SeriesInstanceUID === SeriesInstanceUID + public getDisplaySetsForSeries = ( + seriesInstanceUID: string + ): DisplaySet[] => { + return [...displaySetCache.values()].filter( + displaySet => displaySet.SeriesInstanceUID === seriesInstanceUID ); }; - getDisplaySetForSOPInstanceUID( - SOPInstanceUID, - SeriesInstanceUID, - frameNumber - ) { - const displaySets = SeriesInstanceUID - ? this.getDisplaySetsForSeries(SeriesInstanceUID) - : this.getDisplaySetCache(); + public getDisplaySetForSOPInstanceUID( + sopInstanceUID: string, + seriesInstanceUID: string, + frameNumber?: number + ): DisplaySet { + const displaySets = seriesInstanceUID + ? this.getDisplaySetsForSeries(seriesInstanceUID) + : [...this.getDisplaySetCache().values()]; const displaySet = displaySets.find(ds => { return ( - ds.images && ds.images.some(i => i.SOPInstanceUID === SOPInstanceUID) + ds.images && ds.images.some(i => i.SOPInstanceUID === sopInstanceUID) ); }); return displaySet; } - setDisplaySetMetadataInvalidated(displaySetInstanceUID) { + public setDisplaySetMetadataInvalidated(displaySetInstanceUID: string): void { const displaySet = this.getDisplaySetByUID(displaySetInstanceUID); if (!displaySet) { @@ -117,19 +154,17 @@ export default class DisplaySetService extends PubSubService { ); } - deleteDisplaySet(displaySetInstanceUID) { - const { activeDisplaySets } = this; - - const displaySetCacheIndex = displaySetCache.findIndex( - ds => ds.displaySetInstanceUID === displaySetInstanceUID - ); + public deleteDisplaySet(displaySetInstanceUID) { + if (!displaySetInstanceUID) return; + const { activeDisplaySets, activeDisplaySetsMap } = this; const activeDisplaySetsIndex = activeDisplaySets.findIndex( ds => ds.displaySetInstanceUID === displaySetInstanceUID ); - displaySetCache.splice(displaySetCacheIndex, 1); + displaySetCache.delete(displaySetInstanceUID); activeDisplaySets.splice(activeDisplaySetsIndex, 1); + activeDisplaySetsMap.delete(displaySetInstanceUID); this._broadcastEvent(EVENTS.DISPLAY_SETS_CHANGED, this.activeDisplaySets); this._broadcastEvent(EVENTS.DISPLAY_SETS_REMOVED, { @@ -141,10 +176,8 @@ export default class DisplaySetService extends PubSubService { * @param {string} displaySetInstanceUID * @returns {object} displaySet */ - getDisplaySetByUID = displaySetInstanceUid => - displaySetCache.find( - displaySet => displaySet.displaySetInstanceUID === displaySetInstanceUid - ); + public getDisplaySetByUID = (displaySetInstanceUid: string): DisplaySet => + displaySetCache.get(displaySetInstanceUid); /** * @@ -167,7 +200,7 @@ export default class DisplaySetService extends PubSubService { } // If array of instances => One instance. - let displaySetsAdded = []; + const displaySetsAdded = []; if (batch) { for (let i = 0; i < input.length; i++) { @@ -177,12 +210,12 @@ export default class DisplaySetService extends PubSubService { settings ); - displaySetsAdded = [...displaySetsAdded, displaySets]; + displaySetsAdded.push(...displaySets); } } else { const displaySets = this.makeDisplaySetForInstances(input, settings); - displaySetsAdded = displaySets; + displaySetsAdded.push(...displaySets); } const options = {}; @@ -191,10 +224,13 @@ export default class DisplaySetService extends PubSubService { options.madeInClient = true; } - // TODO: This is tricky. How do we know we're not resetting to the same/existing DSs? - // TODO: This is likely run anytime we touch DicomMetadataStore. How do we prevent unnecessary broadcasts? - if (displaySetsAdded && displaySetsAdded.length) { + if (this.activeDisplaySetsChanged) { + this.activeDisplaySetsChanged = false; this._broadcastEvent(EVENTS.DISPLAY_SETS_CHANGED, this.activeDisplaySets); + } + if (displaySetsAdded?.length) { + // The response from displaySetsAdded will only contain newly added + // display sets. this._broadcastEvent(EVENTS.DISPLAY_SETS_ADDED, { displaySetsAdded, options, @@ -210,22 +246,45 @@ export default class DisplaySetService extends PubSubService { * the mode specific onModeExit is called before this method and should * store the active display sets and the cached data. */ - onModeExit() { - this.getDisplaySetCache().length = 0; + public onModeExit(): void { + this.getDisplaySetCache().clear(); this.activeDisplaySets.length = 0; + this.activeDisplaySetsMap.clear(); } - makeDisplaySetForInstances(instancesSrc, settings) { - let instances = instancesSrc; + /** + * Creates new display sets for the instances contained in instancesSrc + * according to the sop class handlers registered. + * This is idempotent in that calling it a second time with the + * same set of instances will not result in new display sets added. + * However, the response for the subsequent call will be empty as the data + * is already present. + * Calling it with some new instances and some existing instances will + * result in the new instances being added to existing display sets if + * they support the addInstances call, OR to new instances otherwise. + * Only the new instances are returned - the others are updated. + * + * @param instancesSrc are instances to add + * @param settings are settings to add + * @returns Array of the display sets added. + */ + public makeDisplaySetForInstances( + instancesSrc: InstanceMetadata[], + settings + ): DisplaySet[] { + // Some of the sop class handlers take a direct reference to instances + // so make sure it gets copied here so that they have their own ref + let instances = [...instancesSrc]; const instance = instances[0]; const existingDisplaySets = this.getDisplaySetsForSeries(instance.SeriesInstanceUID) || []; const SOPClassHandlerIds = this.SOPClassHandlerIds; - let allDisplaySets; + const allDisplaySets = []; - for (let i = 0; i < SOPClassHandlerIds.length; i++) { + // Iterate over the sop class handlers while there are still instances to add + for (let i = 0; i < SOPClassHandlerIds.length && instances.length; i++) { const SOPClassHandlerId = SOPClassHandlerIds[i]; const handler = this.extensionManager.getModuleEntry(SOPClassHandlerId); @@ -236,34 +295,81 @@ export default class DisplaySetService extends PubSubService { ); if (displaySets.length) { - this._addActiveDisplaySets(displaySets); - } else { - displaySets = handler.getDisplaySetsFromSeries(instances); + // This case occurs when there are already display sets, so remove + // any instances in existing display sets. + instances = filterInstances(instances, displaySets); + // See if an existing display set can add this instance to it, + // for example, if it is a new image to be added to the existing set + for (const ds of displaySets) { + const addedDs = ds.addInstances?.(instances, this); + if (addedDs) { + this.activeDisplaySetsChanged = true; + instances = filterInstances(instances, [addedDs]); + this._addActiveDisplaySets([addedDs]); + this.setDisplaySetMetadataInvalidated( + addedDs.displaySetInstanceUID + ); + } + // This means that all instances already existed or got added to + // existing display sets, and had an invalidated event fired + if (!instances.length) return allDisplaySets; + } - if (!displaySets || !displaySets.length) continue; - - // applying hp-defined viewport settings to the displaysets - displaySets.forEach(ds => { - Object.keys(settings).forEach(key => { - ds[key] = settings[key]; - }); - }); - - this._addDisplaySetsToCache(displaySets); - this._addActiveDisplaySets(displaySets); - - instances = instances.filter( - instance => !findInstance(instance, displaySets) - ); + if (!instances.length) { + // Everything is already added - this is just an update caused + // by something else + this._addActiveDisplaySets(displaySets); + return allDisplaySets; + } } - allDisplaySets = allDisplaySets - ? [...allDisplaySets, ...displaySets] - : displaySets; + // The instances array still contains some instances, so try + // creating additional display sets using the sop class handler + displaySets = handler.getDisplaySetsFromSeries(instances); - if (!instances.length) return allDisplaySets; + if (!displaySets || !displaySets.length) continue; + + // applying hp-defined viewport settings to the displaysets + displaySets.forEach(ds => { + Object.keys(settings).forEach(key => { + ds[key] = settings[key]; + }); + }); + + this._addDisplaySetsToCache(displaySets); + this._addActiveDisplaySets(displaySets); + + // It is possible that this SOP class handler handled some instances + // but there may need to be other instances handled by other handlers, + // so remove the handled instances + instances = filterInstances(instances, displaySets); + + allDisplaySets.push(...displaySets); } } return allDisplaySets; } + + /** + * Iterates over displaysets and invokes comparator for each element. + * It returns a list of items that has being succeed by comparator method. + * + * @param comparator - method to be used on the validation + * @returns list of displaysets + */ + public getDisplaySetsBy(comparator: (DisplaySet) => boolean): DisplaySet[] { + const result = []; + + if (typeof comparator !== 'function') { + throw new Error(`The comparator ${comparator} was not a function`); + } + + this.getActiveDisplaySets().forEach(displaySet => { + if (comparator(displaySet)) { + result.push(displaySet); + } + }); + + return result; + } } diff --git a/platform/core/src/services/HangingProtocolService/HPMatcher.js b/platform/core/src/services/HangingProtocolService/HPMatcher.js index a369f2460..b87c31e84 100644 --- a/platform/core/src/services/HangingProtocolService/HPMatcher.js +++ b/platform/core/src/services/HangingProtocolService/HPMatcher.js @@ -32,7 +32,7 @@ const match = ( // Allow for matching against current or prior specifically const prior = options?.studies?.[1]; const current = options?.studies?.[0]; - const instance = (metadataInstance.images || metadataInstance.others)?.[0]; + const instance = metadataInstance.instances?.[0]; const fromSrc = { prior, current, diff --git a/platform/core/src/types/index.ts b/platform/core/src/types/index.ts index 25df9b028..089a994f5 100644 --- a/platform/core/src/types/index.ts +++ b/platform/core/src/types/index.ts @@ -2,6 +2,7 @@ import * as Extensions from '../extensions/ExtensionManager'; import * as HangingProtocol from './HangingProtocol'; import Services from './Services'; import Hotkey from '../classes/Hotkey'; +import { DisplaySet } from '../services/DisplaySetService/DisplaySetService'; export * from '../services/CustomizationService/types'; // Separate out some generic types @@ -16,4 +17,4 @@ export * from './IPubSub'; * Export the types used within the various services and managers, but * not the services/managers themselves, which are exported at the top level. */ -export { Extensions, HangingProtocol, Services, Hotkey }; +export { Extensions, HangingProtocol, Services, Hotkey, DisplaySet }; diff --git a/platform/viewer/cypress/integration/measurement-tracking/OHIFMeasurementPanel.spec.js b/platform/viewer/cypress/integration/measurement-tracking/OHIFMeasurementPanel.spec.js index 95acd97de..d380d9544 100644 --- a/platform/viewer/cypress/integration/measurement-tracking/OHIFMeasurementPanel.spec.js +++ b/platform/viewer/cypress/integration/measurement-tracking/OHIFMeasurementPanel.spec.js @@ -59,7 +59,9 @@ describe('OHIF Measurement Panel', function() { cy.get('@viewportInfoTopRight').should('contains.text', '(14/'); // Click on first measurement item - cy.get('[data-cy="measurement-item"]').click(); + cy.get('[data-cy="measurement-item"]') + .eq(0) + .click(); cy.get('@viewportInfoTopRight').should('contains.text', '(1/'); cy.get('@viewportInfoTopRight').should('not.contains.text', '(14/'); diff --git a/yarn.lock b/yarn.lock index 5611ea7a2..113a1eb55 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1451,6 +1451,14 @@ detect-gpu "^4.0.45" lodash.clonedeep "4.5.0" +"@cornerstonejs/core@^0.42.2": + version "0.42.2" + resolved "https://registry.yarnpkg.com/@cornerstonejs/core/-/core-0.42.2.tgz#be69adbfd7b63718316a4f18fa55ca473506cee5" + integrity sha512-sLRqCOzR8cxBtQel9fltRti/rQRiYs1Wgx/CaYRPXlWID9Gj9os4j2PJHa70OiMIp4shMsF3jyVW7BPK0t6ZJQ== + dependencies: + detect-gpu "^4.0.45" + lodash.clonedeep "4.5.0" + "@cornerstonejs/streaming-image-volume-loader@^0.16.0": version "0.16.0" resolved "https://registry.npmjs.org/@cornerstonejs/streaming-image-volume-loader/-/streaming-image-volume-loader-0.16.0.tgz#513f868c285963fd2f2dbf54ed7840a2dc05e33a" @@ -1459,12 +1467,12 @@ "@cornerstonejs/core" "^0.40.0" cornerstone-wado-image-loader "^4.10.2" -"@cornerstonejs/tools@^0.60.1": - version "0.60.1" - resolved "https://registry.npmjs.org/@cornerstonejs/tools/-/tools-0.60.1.tgz#88cf32fe79c7fb714a99c1a63c25822233a4d231" - integrity sha512-0GsxN8INh8/1/uKH4pU1ZT8XLNn4Xi2GJug9CQBT6plfnppru//+P+xl+LEQbYVpsydD1iYoWzLe8ykPuIeQCA== +"@cornerstonejs/tools@^0.61.11": + version "0.61.11" + resolved "https://registry.yarnpkg.com/@cornerstonejs/tools/-/tools-0.61.11.tgz#dacd85967cd6ab22c27dd44c10b14664863631f9" + integrity sha512-TCUde2gmuyiyd0EXhoT4DhDZBHYy82MOiekGQe+IG24um3a7GNGJ7jOKBk7fVFxJCTAI2Cb6XI8K79h6BhuWdg== dependencies: - "@cornerstonejs/core" "^0.40.0" + "@cornerstonejs/core" "^0.42.2" lodash.clonedeep "4.5.0" lodash.get "^4.4.2" From 66863281c4e27f93e2f09373594b0e604f1300e3 Mon Sep 17 00:00:00 2001 From: Alireza Date: Wed, 26 Apr 2023 12:21:08 -0400 Subject: [PATCH 14/54] feat(RT): add dicom RT support via volume viewports (#3310) * feat: initial RT support * make the segmentation service work with representation data * feat: make segmentation service work with representations * fix rtss vis * fix: rt hydration * fix the rendering of rt names * fix imports * refactor: Modify status and click handling for hydration of RTStructures Modify status and click handling for hydration of RTStructures by renaming `onPillClick` to `onStatusClick` in `OHIFCornerstoneRTViewport.tsx` and `_getStatusComponent.tsx` files. Also, update initial segmentation configurations in `PanelSegmentation.tsx` and simplify configuration changes and values for segmentation service in `SegmentationService.ts`. Finally, remove console debug in `CornerstoneViewportService.ts`. * wip for highlighting contours * refactor rt displayset code * review code update * update cornerstone dependencies * refactor: Update license year, version number, and minor code cleanup This commit updates the license year in several files, updates the version number in package.json, and contains minor code cleanup in two files. * add bulkdataURI retrieve for RT * fix package version * apply review comments * apply review comments * apply review comments * feat(panels): refactor and streamline segmentation configuration and inputs Rewrote state hooks and streamlined the configuration input for `PanelSegmentation` to be more verbose and reusable. Included several new input types, including the `InputRange` component which now shows a fixed floating value based on the step provided. The `SegmentationConfig` component now works with dynamic values controlled by `initialConfig`. These changes should improve function usability and make the code more maintainable going forward. * fix various bugs * fix contour delete by upgrade cs3d version * feat(viewport, inputNumber, segmentationConfig, orthanc): Implement minimum and maximum values for input number components, and useBulkDataURI for Orthanc configuration. Compare measurement view planes with absolute viewport view planes in Cornerstone viewport. * update yarn lock --- .../.webpack/webpack.dev.js | 8 + .../.webpack/webpack.prod.js | 63 ++ extensions/cornerstone-dicom-rt/LICENSE | 20 + extensions/cornerstone-dicom-rt/README.md | 13 + .../cornerstone-dicom-rt/babel.config.js | 44 ++ extensions/cornerstone-dicom-rt/package.json | 71 ++ .../src/getSopClassHandlerModule.js | 207 ++++++ extensions/cornerstone-dicom-rt/src/id.js | 7 + extensions/cornerstone-dicom-rt/src/index.tsx | 61 ++ .../cornerstone-dicom-rt/src/loadRTStruct.js | 318 ++++++++ .../src/utils/_hydrateRT.ts | 70 ++ .../src/utils/initRTToolGroup.ts | 12 + .../src/utils/promptHydrateRT.ts | 70 ++ .../viewports/OHIFCornerstoneRTViewport.tsx | 415 +++++++++++ .../src/viewports/_getStatusComponent.tsx | 54 ++ extensions/cornerstone-dicom-seg/LICENSE | 2 +- .../src/getSopClassHandlerModule.js | 28 +- .../cornerstone-dicom-seg/src/index.tsx | 13 +- .../src/panels/PanelSegmentation.tsx | 37 +- .../src/panels/segmentationConfigReducer.tsx | 2 - .../src/utils/initSEGToolGroup.ts | 34 +- .../viewports/OHIFCornerstoneSEGViewport.tsx | 47 +- extensions/cornerstone-dicom-sr/package.json | 2 +- extensions/cornerstone/package.json | 4 +- .../src/Viewport/OHIFCornerstoneViewport.tsx | 12 +- .../cornerstone/src/getCustomizationModule.ts | 37 + extensions/cornerstone/src/index.tsx | 4 +- extensions/cornerstone/src/init.tsx | 2 +- .../RTSTRUCT/mapROIContoursToRTStructData.ts | 38 + .../SegmentationService.ts | 699 ++++++++++++------ .../SegmentationServiceTypes.ts | 48 +- .../CornerstoneViewportService.ts | 232 +++--- .../cornerstone/src/utils/transitions.ts | 14 + .../default/src/DicomWebDataSource/index.js | 11 + .../default/src/getSopClassHandlerModule.js | 10 +- extensions/measurement-tracking/package.json | 2 +- modes/longitudinal/package.json | 2 + modes/longitudinal/src/index.js | 14 +- .../src/classes/{ImageSet.js => ImageSet.ts} | 51 +- .../core/src/extensions/ExtensionManager.ts | 1 + platform/core/src/types/Color.ts | 4 + platform/core/src/types/index.ts | 1 + .../services/data/SegmentationService.md | 4 +- .../components/InputNumber/InputNumber.tsx | 37 +- .../src/components/InputRange/InputRange.tsx | 5 +- .../LoadingIndicatorTotalPercent.tsx | 54 ++ .../LoadingIndicatorTotalPercent/index.js | 2 + .../SegmentationConfig.tsx | 137 +--- .../SegmentationGroupTable.tsx | 31 +- .../segmentationConfigReducer.tsx | 22 - platform/ui/src/components/index.js | 2 + platform/ui/src/index.js | 1 + platform/viewer/netlify.toml | 1 - platform/viewer/package.json | 1 + platform/viewer/pluginConfig.json | 6 +- platform/viewer/public/config/default.js | 1 + platform/viewer/public/config/demo.js | 1 + .../viewer/public/config/local_dcm4chee.js | 7 +- .../viewer/public/config/local_orthanc.js | 1 + yarn.lock | 69 +- 60 files changed, 2488 insertions(+), 678 deletions(-) create mode 100644 extensions/cornerstone-dicom-rt/.webpack/webpack.dev.js create mode 100644 extensions/cornerstone-dicom-rt/.webpack/webpack.prod.js create mode 100644 extensions/cornerstone-dicom-rt/LICENSE create mode 100644 extensions/cornerstone-dicom-rt/README.md create mode 100644 extensions/cornerstone-dicom-rt/babel.config.js create mode 100644 extensions/cornerstone-dicom-rt/package.json create mode 100644 extensions/cornerstone-dicom-rt/src/getSopClassHandlerModule.js create mode 100644 extensions/cornerstone-dicom-rt/src/id.js create mode 100644 extensions/cornerstone-dicom-rt/src/index.tsx create mode 100644 extensions/cornerstone-dicom-rt/src/loadRTStruct.js create mode 100644 extensions/cornerstone-dicom-rt/src/utils/_hydrateRT.ts create mode 100644 extensions/cornerstone-dicom-rt/src/utils/initRTToolGroup.ts create mode 100644 extensions/cornerstone-dicom-rt/src/utils/promptHydrateRT.ts create mode 100644 extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx create mode 100644 extensions/cornerstone-dicom-rt/src/viewports/_getStatusComponent.tsx create mode 100644 extensions/cornerstone/src/getCustomizationModule.ts create mode 100644 extensions/cornerstone/src/services/SegmentationService/RTSTRUCT/mapROIContoursToRTStructData.ts rename platform/core/src/classes/{ImageSet.js => ImageSet.ts} (72%) create mode 100644 platform/core/src/types/Color.ts create mode 100644 platform/ui/src/components/LoadingIndicatorTotalPercent/LoadingIndicatorTotalPercent.tsx create mode 100644 platform/ui/src/components/LoadingIndicatorTotalPercent/index.js delete mode 100644 platform/ui/src/components/SegmentationGroupTable/segmentationConfigReducer.tsx diff --git a/extensions/cornerstone-dicom-rt/.webpack/webpack.dev.js b/extensions/cornerstone-dicom-rt/.webpack/webpack.dev.js new file mode 100644 index 000000000..1ae308448 --- /dev/null +++ b/extensions/cornerstone-dicom-rt/.webpack/webpack.dev.js @@ -0,0 +1,8 @@ +const path = require('path'); +const webpackCommon = require('./../../../.webpack/webpack.commonjs.js'); +const SRC_DIR = path.join(__dirname, '../src'); +const DIST_DIR = path.join(__dirname, '../dist'); + +module.exports = (env, argv) => { + return webpackCommon(env, argv, { SRC_DIR, DIST_DIR }); +}; diff --git a/extensions/cornerstone-dicom-rt/.webpack/webpack.prod.js b/extensions/cornerstone-dicom-rt/.webpack/webpack.prod.js new file mode 100644 index 000000000..070a723e3 --- /dev/null +++ b/extensions/cornerstone-dicom-rt/.webpack/webpack.prod.js @@ -0,0 +1,63 @@ +const path = require('path'); +const pkg = require('../package.json'); + +const outputFile = 'index.umd.js'; +const rootDir = path.resolve(__dirname, '../'); +const outputFolder = path.join(__dirname, `../dist/umd/${pkg.name}/`); + +// Todo: add ESM build for the extension in addition to umd build + +const config = { + mode: 'production', + entry: rootDir + '/' + pkg.module, + devtool: 'source-map', + output: { + path: outputFolder, + filename: outputFile, + library: pkg.name, + libraryTarget: 'umd', + chunkFilename: '[name].chunk.js', + umdNamedDefine: true, + globalObject: "typeof self !== 'undefined' ? self : this", + }, + externals: [ + { + react: { + root: 'React', + commonjs2: 'react', + commonjs: 'react', + amd: 'react', + }, + '@ohif/core': { + commonjs2: '@ohif/core', + commonjs: '@ohif/core', + amd: '@ohif/core', + root: '@ohif/core', + }, + '@ohif/ui': { + commonjs2: '@ohif/ui', + commonjs: '@ohif/ui', + amd: '@ohif/ui', + root: '@ohif/ui', + }, + }, + ], + module: { + rules: [ + { + test: /(\.jsx|\.js|\.tsx|\.ts)$/, + loader: 'babel-loader', + exclude: /(node_modules|bower_components)/, + resolve: { + extensions: ['.js', '.jsx', '.ts', '.tsx'], + }, + }, + ], + }, + resolve: { + modules: [path.resolve('./node_modules'), path.resolve('./src')], + extensions: ['.json', '.js', '.jsx', '.tsx', '.ts'], + }, +}; + +module.exports = config; diff --git a/extensions/cornerstone-dicom-rt/LICENSE b/extensions/cornerstone-dicom-rt/LICENSE new file mode 100644 index 000000000..983c5ef34 --- /dev/null +++ b/extensions/cornerstone-dicom-rt/LICENSE @@ -0,0 +1,20 @@ +MIT License + +Copyright (c) 2023 Open Health Imaging Foundation + +Permission is hereby granted, free of charge, to any person obtaining a copy of +this software and associated documentation files (the "Software"), to deal in +the Software without restriction, including without limitation the rights to +use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of +the Software, and to permit persons to whom the Software is furnished to do so, +subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS +FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR +COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER +IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/extensions/cornerstone-dicom-rt/README.md b/extensions/cornerstone-dicom-rt/README.md new file mode 100644 index 000000000..a23ee416f --- /dev/null +++ b/extensions/cornerstone-dicom-rt/README.md @@ -0,0 +1,13 @@ +# dicom-rt +## Description + +DICOM RT read workflow. This extension will allow you to load a DICOM RTSS image +and display it in OHIF. + + +## Author + +OHIF + +## License +MIT diff --git a/extensions/cornerstone-dicom-rt/babel.config.js b/extensions/cornerstone-dicom-rt/babel.config.js new file mode 100644 index 000000000..92fbbdeaf --- /dev/null +++ b/extensions/cornerstone-dicom-rt/babel.config.js @@ -0,0 +1,44 @@ +module.exports = { + plugins: ['inline-react-svg', '@babel/plugin-proposal-class-properties'], + env: { + test: { + presets: [ + [ + // TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2 + '@babel/preset-env', + { + modules: 'commonjs', + debug: false, + }, + "@babel/preset-typescript", + ], + '@babel/preset-react', + ], + plugins: [ + '@babel/plugin-proposal-object-rest-spread', + '@babel/plugin-syntax-dynamic-import', + '@babel/plugin-transform-regenerator', + '@babel/plugin-transform-runtime', + ], + }, + production: { + presets: [ + // WebPack handles ES6 --> Target Syntax + ['@babel/preset-env', { modules: false }], + '@babel/preset-react', + "@babel/preset-typescript", + ], + ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'], + }, + development: { + presets: [ + // WebPack handles ES6 --> Target Syntax + ['@babel/preset-env', { modules: false }], + '@babel/preset-react', + "@babel/preset-typescript", + ], + plugins: ['react-hot-loader/babel'], + ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'], + }, + }, +}; diff --git a/extensions/cornerstone-dicom-rt/package.json b/extensions/cornerstone-dicom-rt/package.json new file mode 100644 index 000000000..cd4bcdb6c --- /dev/null +++ b/extensions/cornerstone-dicom-rt/package.json @@ -0,0 +1,71 @@ +{ + "name": "@ohif/extension-cornerstone-dicom-rt", + "version": "3.0.0", + "description": "DICOM RT read workflow", + "author": "OHIF", + "license": "MIT", + "main": "dist/umd/@ohif/dicom-rt/index.umd.js", + "module": "src/index.tsx", + "files": [ + "dist/**", + "public/**", + "README.md" + ], + "repository": "OHIF/Viewers", + "keywords": [ + "ohif-extension" + ], + "engines": { + "node": ">=14", + "npm": ">=6", + "yarn": ">=1.18.0" + }, + "scripts": { + "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo", + "dev:dicom-seg": "yarn run dev", + "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js", + "build:package": "yarn run build", + "start": "yarn run dev" + }, + "peerDependencies": { + "@ohif/core": "^3.0.0", + "@ohif/extension-default": "^3.0.0", + "@ohif/extension-cornerstone": "^3.0.0", + "@ohif/i18n": "^1.0.0", + "prop-types": "^15.6.2", + "react": "^17.0.2", + "react-dom": "^17.0.2", + "react-i18next": "^10.11.0", + "react-router": "^6.3.0", + "react-router-dom": "^6.3.0", + "webpack": "^5.50.0", + "webpack-merge": "^5.7.3" + }, + "dependencies": { + "@babel/runtime": "7.7.6", + "react-color": "^2.19.3" + }, + "devDependencies": { + "@babel/core": "^7.5.0", + "@babel/plugin-proposal-class-properties": "^7.5.0", + "@babel/plugin-proposal-object-rest-spread": "^7.5.5", + "@babel/plugin-syntax-dynamic-import": "^7.2.0", + "@babel/plugin-transform-arrow-functions": "^7.2.0", + "@babel/plugin-transform-regenerator": "^7.4.5", + "@babel/plugin-transform-runtime": "^7.5.0", + "babel-plugin-inline-react-svg": "^2.0.1", + "@babel/preset-env": "^7.5.0", + "@babel/preset-react": "^7.0.0", + "babel-eslint": "^8.0.3", + "babel-loader": "^8.0.0-beta.4", + "clean-webpack-plugin": "^4.0.0", + "copy-webpack-plugin": "^10.2.0", + "cross-env": "^7.0.3", + "dotenv": "^14.1.0", + "eslint": "^5.0.1", + "eslint-loader": "^2.0.0", + "webpack": "^5.50.0", + "webpack-merge": "^5.7.3", + "webpack-cli": "^4.7.2" + } +} diff --git a/extensions/cornerstone-dicom-rt/src/getSopClassHandlerModule.js b/extensions/cornerstone-dicom-rt/src/getSopClassHandlerModule.js new file mode 100644 index 000000000..81ba6aab9 --- /dev/null +++ b/extensions/cornerstone-dicom-rt/src/getSopClassHandlerModule.js @@ -0,0 +1,207 @@ +import { utils } from '@ohif/core'; + +import { SOPClassHandlerId } from './id'; +import loadRTStruct from './loadRTStruct'; + +const sopClassUids = ['1.2.840.10008.5.1.4.1.1.481.3']; + +let loadPromises = {}; + +function _getDisplaySetsFromSeries( + instances, + servicesManager, + extensionManager +) { + const instance = instances[0]; + + const { + StudyInstanceUID, + SeriesInstanceUID, + SOPInstanceUID, + SeriesDescription, + SeriesNumber, + SeriesDate, + SOPClassUID, + wadoRoot, + wadoUri, + wadoUriRoot, + } = instance; + + const displaySet = { + Modality: 'RTSTRUCT', + loading: false, + isReconstructable: false, // by default for now since it is a volumetric SEG currently + displaySetInstanceUID: utils.guid(), + SeriesDescription, + SeriesNumber, + SeriesDate, + SOPInstanceUID, + SeriesInstanceUID, + StudyInstanceUID, + SOPClassHandlerId, + SOPClassUID, + referencedImages: null, + referencedSeriesInstanceUID: null, + referencedDisplaySetInstanceUID: null, + isDerivedDisplaySet: true, + isLoaded: false, + isHydrated: false, + structureSet: null, + sopClassUids, + instance, + wadoRoot, + wadoUriRoot, + wadoUri, + isOverlayDisplaySet: true, + }; + + let referencedSeriesSequence = instance.ReferencedSeriesSequence; + if ( + instance.ReferencedFrameOfReferenceSequence && + !instance.ReferencedSeriesSequence + ) { + instance.ReferencedSeriesSequence = _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence( + instance.ReferencedFrameOfReferenceSequence + ); + referencedSeriesSequence = instance.ReferencedSeriesSequence; + } + + if (!referencedSeriesSequence) { + throw new Error('ReferencedSeriesSequence is missing for the RTSTRUCT'); + } + + const referencedSeries = referencedSeriesSequence[0]; + + displaySet.referencedImages = + instance.ReferencedSeriesSequence.ReferencedInstanceSequence; + displaySet.referencedSeriesInstanceUID = referencedSeries.SeriesInstanceUID; + + displaySet.getReferenceDisplaySet = () => { + const { DisplaySetService } = servicesManager.services; + const referencedDisplaySets = DisplaySetService.getDisplaySetsForSeries( + displaySet.referencedSeriesInstanceUID + ); + + if (!referencedDisplaySets || referencedDisplaySets.length === 0) { + throw new Error('Referenced DisplaySet is missing for the RT'); + } + + const referencedDisplaySet = referencedDisplaySets[0]; + + displaySet.referencedDisplaySetInstanceUID = + referencedDisplaySet.displaySetInstanceUID; + + return referencedDisplaySet; + }; + + displaySet.load = ({ headers }) => + _load(displaySet, servicesManager, extensionManager, headers); + + return [displaySet]; +} + +function _load(rtDisplaySet, servicesManager, extensionManager, headers) { + const { SOPInstanceUID } = rtDisplaySet; + const { segmentationService } = servicesManager.services; + if ( + (rtDisplaySet.loading || rtDisplaySet.isLoaded) && + loadPromises[SOPInstanceUID] && + _segmentationExistsInCache(rtDisplaySet, segmentationService) + ) { + return loadPromises[SOPInstanceUID]; + } + + rtDisplaySet.loading = true; + + // We don't want to fire multiple loads, so we'll wait for the first to finish + // and also return the same promise to any other callers. + loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => { + if (!rtDisplaySet.structureSet) { + const structureSet = await loadRTStruct( + extensionManager, + rtDisplaySet, + rtDisplaySet.getReferenceDisplaySet(), + headers + ); + + rtDisplaySet.structureSet = structureSet; + } + + const suppressEvents = true; + segmentationService + .createSegmentationForRTDisplaySet(rtDisplaySet, null, suppressEvents) + .then(() => { + rtDisplaySet.loading = false; + resolve(); + }) + .catch(error => { + rtDisplaySet.loading = false; + reject(error); + }); + }); + + return loadPromises[SOPInstanceUID]; +} + +function _deriveReferencedSeriesSequenceFromFrameOfReferenceSequence( + ReferencedFrameOfReferenceSequence +) { + const ReferencedSeriesSequence = []; + + ReferencedFrameOfReferenceSequence.forEach(referencedFrameOfReference => { + const { RTReferencedStudySequence } = referencedFrameOfReference; + + RTReferencedStudySequence.forEach(rtReferencedStudy => { + const { RTReferencedSeriesSequence } = rtReferencedStudy; + + RTReferencedSeriesSequence.forEach(rtReferencedSeries => { + const ReferencedInstanceSequence = []; + const { ContourImageSequence, SeriesInstanceUID } = rtReferencedSeries; + + ContourImageSequence.forEach(contourImage => { + ReferencedInstanceSequence.push({ + ReferencedSOPInstanceUID: contourImage.ReferencedSOPInstanceUID, + ReferencedSOPClassUID: contourImage.ReferencedSOPClassUID, + }); + }); + + const referencedSeries = { + SeriesInstanceUID, + ReferencedInstanceSequence, + }; + + ReferencedSeriesSequence.push(referencedSeries); + }); + }); + }); + + return ReferencedSeriesSequence; +} + +function _segmentationExistsInCache(rtDisplaySet, segmentationService) { + // Todo: fix this + return false; + // This should be abstracted with the CornerstoneCacheService + const rtContourId = rtDisplaySet.displaySetInstanceUID; + const contour = segmentationService.getContour(rtContourId); + + return contour !== undefined; +} + +function getSopClassHandlerModule({ servicesManager, extensionManager }) { + return [ + { + name: 'dicom-rt', + sopClassUids, + getDisplaySetsFromSeries: instances => { + return _getDisplaySetsFromSeries( + instances, + servicesManager, + extensionManager + ); + }, + }, + ]; +} + +export default getSopClassHandlerModule; diff --git a/extensions/cornerstone-dicom-rt/src/id.js b/extensions/cornerstone-dicom-rt/src/id.js new file mode 100644 index 000000000..2c8691f0b --- /dev/null +++ b/extensions/cornerstone-dicom-rt/src/id.js @@ -0,0 +1,7 @@ +import packageJson from '../package.json'; + +const id = packageJson.name; +const SOPClassHandlerName = 'dicom-rt'; +const SOPClassHandlerId = `${id}.sopClassHandlerModule.${SOPClassHandlerName}`; + +export { id, SOPClassHandlerId, SOPClassHandlerName }; diff --git a/extensions/cornerstone-dicom-rt/src/index.tsx b/extensions/cornerstone-dicom-rt/src/index.tsx new file mode 100644 index 000000000..7d5529776 --- /dev/null +++ b/extensions/cornerstone-dicom-rt/src/index.tsx @@ -0,0 +1,61 @@ +import { id } from './id'; +import React from 'react'; +import { Types } from '@ohif/core'; +import getSopClassHandlerModule from './getSopClassHandlerModule'; + +const Component = React.lazy(() => { + return import( + /* webpackPrefetch: true */ './viewports/OHIFCornerstoneRTViewport' + ); +}); + +const OHIFCornerstoneRTViewport = props => { + return ( + Loading...}> + + + ); +}; + +/** + * You can remove any of the following modules if you don't need them. + */ +const extension: Types.Extensions.Extension = { + /** + * Only required property. Should be a unique value across all extensions. + * You ID can be anything you want, but it should be unique. + */ + id, + + /** + * PanelModule should provide a list of panels that will be available in OHIF + * for Modes to consume and render. Each panel is defined by a {name, + * iconName, iconLabel, label, component} object. Example of a panel module + * is the StudyBrowserPanel that is provided by the default extension in OHIF. + */ + getViewportModule({ + servicesManager, + extensionManager, + }: Types.Extensions.ExtensionParams) { + const ExtendedOHIFCornerstoneRTViewport = props => { + return ( + + ); + }; + + return [{ name: 'dicom-rt', component: ExtendedOHIFCornerstoneRTViewport }]; + }, + /** + * SopClassHandlerModule should provide a list of sop class handlers that will be + * available in OHIF for Modes to consume and use to create displaySets from Series. + * Each sop class handler is defined by a { name, sopClassUids, getDisplaySetsFromSeries}. + * Examples include the default sop class handler provided by the default extension + */ + getSopClassHandlerModule, +}; + +export default extension; diff --git a/extensions/cornerstone-dicom-rt/src/loadRTStruct.js b/extensions/cornerstone-dicom-rt/src/loadRTStruct.js new file mode 100644 index 000000000..52e1bd7c7 --- /dev/null +++ b/extensions/cornerstone-dicom-rt/src/loadRTStruct.js @@ -0,0 +1,318 @@ +import dcmjs from 'dcmjs'; +const { DicomMessage, DicomMetaDictionary } = dcmjs.data; +const dicomlab2RGB = dcmjs.data.Colors.dicomlab2RGB; + +async function checkAndLoadContourData(instance, datasource) { + if (!instance || !instance.ROIContourSequence) { + return Promise.reject('Invalid instance object or ROIContourSequence'); + } + + const promises = []; + let counter = 0; + + for (const ROIContour of instance.ROIContourSequence) { + if (!ROIContour || !ROIContour.ContourSequence) { + return Promise.reject('Invalid ROIContour or ContourSequence'); + } + + for (const Contour of ROIContour.ContourSequence) { + if (!Contour || !Contour.ContourData) { + return Promise.reject('Invalid Contour or ContourData'); + } + + const contourData = Contour.ContourData; + counter++; + if (Array.isArray(contourData)) { + promises.push(Promise.resolve(contourData)); + } else if (contourData && contourData.BulkDataURI) { + const bulkDataURI = contourData.BulkDataURI; + + if ( + !datasource || + !datasource.retrieve || + !datasource.retrieve.bulkDataURI + ) { + return Promise.reject( + 'Invalid datasource object or retrieve function' + ); + } + + const bulkDataPromise = datasource.retrieve.bulkDataURI({ + BulkDataURI: bulkDataURI, + StudyInstanceUID: instance.StudyInstanceUID, + SeriesInstanceUID: instance.SeriesInstanceUID, + SOPInstanceUID: instance.SOPInstanceUID, + }); + + promises.push(bulkDataPromise); + } else { + return Promise.reject(`Invalid ContourData: ${contourData}`); + } + } + } + const flattenedPromises = promises.flat(); + const resolvedPromises = await Promise.allSettled(flattenedPromises); + + // Modify contourData and replace it in its corresponding ROIContourSequence's Contour's contourData + let index = 0; + instance.ROIContourSequence.forEach((ROIContour, roiIndex) => { + ROIContour.ContourSequence.forEach((Contour, contourIndex) => { + const promise = resolvedPromises[index++]; + + if (promise.status === 'fulfilled') { + const uint8Array = new Uint8Array(promise.value); + const textDecoder = new TextDecoder(); + const dataUint8Array = textDecoder.decode(uint8Array); + if ( + typeof dataUint8Array === 'string' && + dataUint8Array.includes('\\') + ) { + const numSlashes = (dataUint8Array.match(/\\/g) || []).length; + let startIndex = 0; + let endIndex = dataUint8Array.indexOf('\\', startIndex); + let numbersParsed = 0; + const ContourData = []; + + while (numbersParsed !== numSlashes + 1) { + const str = dataUint8Array.substring(startIndex, endIndex); + let value = parseFloat(str); + + ContourData.push(value); + startIndex = endIndex + 1; + endIndex = dataUint8Array.indexOf('\\', startIndex); + endIndex === -1 ? (endIndex = dataUint8Array.length) : endIndex; + numbersParsed++; + } + Contour.ContourData = ContourData; + } else { + Contour.ContourData = []; + } + } else { + console.error(promise.reason); + } + }); + }); +} + +export default async function loadRTStruct( + extensionManager, + rtStructDisplaySet, + referencedDisplaySet, + headers +) { + const utilityModule = extensionManager.getModuleEntry( + '@ohif/extension-cornerstone.utilityModule.common' + ); + const dataSource = extensionManager.getActiveDataSource()[0]; + const { useBulkDataURI } = dataSource.getConfig?.() || {}; + + const { dicomLoaderService } = utilityModule.exports; + const imageIdSopInstanceUidPairs = _getImageIdSopInstanceUidPairsForDisplaySet( + referencedDisplaySet + ); + + // Set here is loading is asynchronous. + // If this function throws its set back to false. + rtStructDisplaySet.isLoaded = true; + let instance = rtStructDisplaySet.instance; + + if (!useBulkDataURI) { + const segArrayBuffer = await dicomLoaderService.findDicomDataPromise( + rtStructDisplaySet, + null, + headers + ); + + const dicomData = DicomMessage.readFile(segArrayBuffer); + const rtStructDataset = DicomMetaDictionary.naturalizeDataset( + dicomData.dict + ); + rtStructDataset._meta = DicomMetaDictionary.namifyDataset(dicomData.meta); + instance = rtStructDataset; + } else { + await checkAndLoadContourData(instance, dataSource); + } + + const { + StructureSetROISequence, + ROIContourSequence, + RTROIObservationsSequence, + } = instance; + + // Define our structure set entry and add it to the rtstruct module state. + const structureSet = { + StructureSetLabel: instance.StructureSetLabel, + SeriesInstanceUID: instance.SeriesInstanceUID, + ROIContours: [], + visible: true, + }; + + for (let i = 0; i < ROIContourSequence.length; i++) { + const ROIContour = ROIContourSequence[i]; + const { ContourSequence } = ROIContour; + + if (!ContourSequence) { + continue; + } + + const isSupported = false; + + const ContourSequenceArray = _toArray(ContourSequence); + + const contourPoints = []; + for (let c = 0; c < ContourSequenceArray.length; c++) { + const { + ContourImageSequence, + ContourData, + NumberOfContourPoints, + ContourGeometricType, + } = ContourSequenceArray[c]; + + const sopInstanceUID = ContourImageSequence.ReferencedSOPInstanceUID; + const imageId = _getImageId(imageIdSopInstanceUidPairs, sopInstanceUID); + + if (!imageId) { + continue; + } + let isSupported = false; + + const points = []; + for (let p = 0; p < NumberOfContourPoints * 3; p += 3) { + points.push({ + x: ContourData[p], + y: ContourData[p + 1], + z: ContourData[p + 2], + }); + } + + switch (ContourGeometricType) { + case 'CLOSED_PLANAR': + case 'OPEN_PLANAR': + case 'POINT': + isSupported = true; + + break; + default: + continue; + } + + contourPoints.push({ + numberOfPoints: NumberOfContourPoints, + points, + type: ContourGeometricType, + isSupported, + }); + } + + _setROIContourMetadata( + structureSet, + StructureSetROISequence, + RTROIObservationsSequence, + ROIContour, + contourPoints, + isSupported + ); + } + return structureSet; +} + +const _getImageId = (imageIdSopInstanceUidPairs, sopInstanceUID) => { + const imageIdSopInstanceUidPairsEntry = imageIdSopInstanceUidPairs.find( + imageIdSopInstanceUidPairsEntry => + imageIdSopInstanceUidPairsEntry.sopInstanceUID === sopInstanceUID + ); + + return imageIdSopInstanceUidPairsEntry + ? imageIdSopInstanceUidPairsEntry.imageId + : null; +}; + +function _getImageIdSopInstanceUidPairsForDisplaySet(referencedDisplaySet) { + return referencedDisplaySet.images.map(image => { + return { + imageId: image.imageId, + sopInstanceUID: image.SOPInstanceUID, + }; + }); +} + +function _setROIContourMetadata( + structureSet, + StructureSetROISequence, + RTROIObservationsSequence, + ROIContour, + contourPoints, + isSupported +) { + const StructureSetROI = StructureSetROISequence.find( + structureSetROI => + structureSetROI.ROINumber === ROIContour.ReferencedROINumber + ); + + const ROIContourData = { + ROINumber: StructureSetROI.ROINumber, + ROIName: StructureSetROI.ROIName, + ROIGenerationAlgorithm: StructureSetROI.ROIGenerationAlgorithm, + ROIDescription: StructureSetROI.ROIDescription, + isSupported, + contourPoints, + visible: true, + }; + + _setROIContourDataColor(ROIContour, ROIContourData); + + if (RTROIObservationsSequence) { + // If present, add additional RTROIObservations metadata. + _setROIContourRTROIObservations( + ROIContourData, + RTROIObservationsSequence, + ROIContour.ReferencedROINumber + ); + } + + structureSet.ROIContours.push(ROIContourData); +} + +function _setROIContourDataColor(ROIContour, ROIContourData) { + let { ROIDisplayColor, RecommendedDisplayCIELabValue } = ROIContour; + + if (!ROIDisplayColor && RecommendedDisplayCIELabValue) { + // If ROIDisplayColor is absent, try using the RecommendedDisplayCIELabValue color. + ROIDisplayColor = dicomlab2RGB(RecommendedDisplayCIELabValue); + } + + if (ROIDisplayColor) { + ROIContourData.colorArray = [...ROIDisplayColor]; + } +} + +function _setROIContourRTROIObservations( + ROIContourData, + RTROIObservationsSequence, + ROINumber +) { + const RTROIObservations = RTROIObservationsSequence.find( + RTROIObservations => RTROIObservations.ReferencedROINumber === ROINumber + ); + + if (RTROIObservations) { + // Deep copy so we don't keep the reference to the dcmjs dataset entry. + const { + ObservationNumber, + ROIObservationDescription, + RTROIInterpretedType, + ROIInterpreter, + } = RTROIObservations; + + ROIContourData.RTROIObservations = { + ObservationNumber, + ROIObservationDescription, + RTROIInterpretedType, + ROIInterpreter, + }; + } +} + +function _toArray(objOrArray) { + return Array.isArray(objOrArray) ? objOrArray : [objOrArray]; +} diff --git a/extensions/cornerstone-dicom-rt/src/utils/_hydrateRT.ts b/extensions/cornerstone-dicom-rt/src/utils/_hydrateRT.ts new file mode 100644 index 000000000..0668c894b --- /dev/null +++ b/extensions/cornerstone-dicom-rt/src/utils/_hydrateRT.ts @@ -0,0 +1,70 @@ +async function _hydrateRTDisplaySet({ + rtDisplaySet, + viewportIndex, + servicesManager, +}) { + const { + segmentationService, + hangingProtocolService, + viewportGridService, + } = servicesManager.services; + + const displaySetInstanceUID = rtDisplaySet.referencedDisplaySetInstanceUID; + + let segmentationId = null; + + // We need the hydration to notify panels about the new segmentation added + const suppressEvents = false; + + segmentationId = await segmentationService.createSegmentationForRTDisplaySet( + rtDisplaySet, + segmentationId, + suppressEvents + ); + + segmentationService.hydrateSegmentation(rtDisplaySet.displaySetInstanceUID); + + const { viewports } = viewportGridService.getState(); + + const updatedViewports = hangingProtocolService.getViewportsRequireUpdate( + viewportIndex, + displaySetInstanceUID + ); + + viewportGridService.setDisplaySetsForViewports(updatedViewports); + + // Todo: fix this after we have a better way for stack viewport segmentations + + // check every viewport in the viewports to see if the displaySetInstanceUID + // is being displayed, if so we need to update the viewport to use volume viewport + // (if already is not using it) since Cornerstone3D currently only supports + // volume viewport for segmentation + viewports.forEach((viewport, index) => { + if (index === viewportIndex) { + return; + } + + const shouldDisplaySeg = segmentationService.shouldRenderSegmentation( + viewport.displaySetInstanceUIDs, + rtDisplaySet.displaySetInstanceUID + ); + + if (shouldDisplaySeg) { + updatedViewports.push({ + viewportIndex: index, + displaySetInstanceUIDs: viewport.displaySetInstanceUIDs, + viewportOptions: { + initialImageOptions: { + preset: 'middle', + }, + }, + }); + } + }); + + // Do the entire update at once + viewportGridService.setDisplaySetsForViewports(updatedViewports); + return true; +} + +export default _hydrateRTDisplaySet; diff --git a/extensions/cornerstone-dicom-rt/src/utils/initRTToolGroup.ts b/extensions/cornerstone-dicom-rt/src/utils/initRTToolGroup.ts new file mode 100644 index 000000000..826e3b9a6 --- /dev/null +++ b/extensions/cornerstone-dicom-rt/src/utils/initRTToolGroup.ts @@ -0,0 +1,12 @@ +function createRTToolGroupAndAddTools( + ToolGroupService, + customizationService, + toolGroupId +) { + const { tools } = + customizationService.get('cornerstone.overlayViewportTools') ?? {}; + + return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools, {}); +} + +export default createRTToolGroupAndAddTools; diff --git a/extensions/cornerstone-dicom-rt/src/utils/promptHydrateRT.ts b/extensions/cornerstone-dicom-rt/src/utils/promptHydrateRT.ts new file mode 100644 index 000000000..4af78caee --- /dev/null +++ b/extensions/cornerstone-dicom-rt/src/utils/promptHydrateRT.ts @@ -0,0 +1,70 @@ +import hydrateRTDisplaySet from './_hydrateRT'; + +const RESPONSE = { + NO_NEVER: -1, + CANCEL: 0, + HYDRATE_SEG: 5, +}; + +function promptHydrateRT({ + servicesManager, + rtDisplaySet, + viewportIndex, + toolGroupId = 'default', +}) { + const { uiViewportDialogService } = servicesManager.services; + + return new Promise(async function(resolve, reject) { + const promptResult = await _askHydrate( + uiViewportDialogService, + viewportIndex + ); + + if (promptResult === RESPONSE.HYDRATE_SEG) { + const isHydrated = await hydrateRTDisplaySet({ + rtDisplaySet, + viewportIndex, + toolGroupId, + servicesManager, + }); + + resolve(isHydrated); + } + }); +} + +function _askHydrate(uiViewportDialogService, viewportIndex) { + return new Promise(function(resolve, reject) { + const message = 'Do you want to open this Segmentation?'; + const actions = [ + { + type: 'secondary', + text: 'No', + value: RESPONSE.CANCEL, + }, + { + type: 'primary', + text: 'Yes', + value: RESPONSE.HYDRATE_SEG, + }, + ]; + const onSubmit = result => { + uiViewportDialogService.hide(); + resolve(result); + }; + + uiViewportDialogService.show({ + viewportIndex, + type: 'info', + message, + actions, + onSubmit, + onOutsideClick: () => { + uiViewportDialogService.hide(); + resolve(RESPONSE.CANCEL); + }, + }); + }); +} + +export default promptHydrateRT; diff --git a/extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx b/extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx new file mode 100644 index 000000000..29adb47d5 --- /dev/null +++ b/extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx @@ -0,0 +1,415 @@ +import React, { useCallback, useEffect, useRef, useState } from 'react'; +import PropTypes from 'prop-types'; +import OHIF, { utils } from '@ohif/core'; +import { + Notification, + ViewportActionBar, + useViewportGrid, + useViewportDialog, + LoadingIndicatorTotalPercent, +} from '@ohif/ui'; + +import _hydrateRTdisplaySet from '../utils/_hydrateRT'; +import promptHydrateRT from '../utils/promptHydrateRT'; +import _getStatusComponent from './_getStatusComponent'; +import createRTToolGroupAndAddTools from '../utils/initRTToolGroup'; +import _hydrateRTDisplaySet from '../utils/_hydrateRT'; + +const { formatDate } = utils; +const RT_TOOLGROUP_BASE_NAME = 'RTToolGroup'; + +function OHIFCornerstoneRTViewport(props) { + const { + children, + displaySets, + viewportOptions, + viewportIndex, + viewportLabel, + servicesManager, + extensionManager, + } = props; + + const { + displaySetService, + toolGroupService, + segmentationService, + uiNotificationService, + customizationService, + } = servicesManager.services; + + const toolGroupId = `${RT_TOOLGROUP_BASE_NAME}-${viewportIndex}`; + + // RT viewport will always have a single display set + if (displaySets.length > 1) { + throw new Error('RT viewport should only have a single display set'); + } + + const rtDisplaySet = displaySets[0]; + + const [viewportGrid, viewportGridService] = useViewportGrid(); + const [viewportDialogState, viewportDialogApi] = useViewportDialog(); + + // States + const [isToolGroupCreated, setToolGroupCreated] = useState(false); + const [selectedSegment, setSelectedSegment] = useState(1); + + // Hydration means that the RT is opened and segments are loaded into the + // segmentation panel, and RT is also rendered on any viewport that is in the + // same frameOfReferenceUID as the referencedSeriesUID of the RT. However, + // loading basically means RT loading over network and bit unpacking of the + // RT data. + const [isHydrated, setIsHydrated] = useState(rtDisplaySet.isHydrated); + const [rtIsLoading, setRtIsLoading] = useState(!rtDisplaySet.isLoaded); + const [element, setElement] = useState(null); + const [processingProgress, setProcessingProgress] = useState({ + percentComplete: null, + totalSegments: null, + }); + + // refs + const referencedDisplaySetRef = useRef(null); + + const { viewports, activeViewportIndex } = viewportGrid; + + const referencedDisplaySet = rtDisplaySet.getReferenceDisplaySet(); + const referencedDisplaySetMetadata = _getReferencedDisplaySetMetadata( + referencedDisplaySet + ); + + referencedDisplaySetRef.current = { + displaySet: referencedDisplaySet, + metadata: referencedDisplaySetMetadata, + }; + /** + * OnElementEnabled callback which is called after the cornerstoneExtension + * has enabled the element. Note: we delegate all the image rendering to + * cornerstoneExtension, so we don't need to do anything here regarding + * the image rendering, element enabling etc. + */ + const onElementEnabled = evt => { + setElement(evt.detail.element); + }; + + const onElementDisabled = () => { + setElement(null); + }; + + const getCornerstoneViewport = useCallback(() => { + const { component: Component } = extensionManager.getModuleEntry( + '@ohif/extension-cornerstone.viewportModule.cornerstone' + ); + + const { + displaySet: referencedDisplaySet, + } = referencedDisplaySetRef.current; + + // Todo: jump to the center of the first segment + return ( + + ); + }, [viewportIndex, rtDisplaySet, toolGroupId]); + + const onSegmentChange = useCallback( + direction => { + direction = direction === 'left' ? -1 : 1; + const segmentationId = rtDisplaySet.displaySetInstanceUID; + const segmentation = segmentationService.getSegmentation(segmentationId); + + const { segments } = segmentation; + + const numberOfSegments = Object.keys(segments).length; + + let newSelectedSegmentIndex = selectedSegment + direction; + + // Segment 0 is always background + if (newSelectedSegmentIndex >= numberOfSegments - 1) { + newSelectedSegmentIndex = 1; + } else if (newSelectedSegmentIndex === 0) { + newSelectedSegmentIndex = numberOfSegments - 1; + } + + segmentationService.jumpToSegmentCenter( + segmentationId, + newSelectedSegmentIndex, + toolGroupId + ); + setSelectedSegment(newSelectedSegmentIndex); + }, + [selectedSegment] + ); + + useEffect(() => { + if (rtIsLoading) { + return; + } + + promptHydrateRT({ + servicesManager, + viewportIndex, + rtDisplaySet, + }).then(isHydrated => { + if (isHydrated) { + setIsHydrated(true); + } + }); + }, [servicesManager, viewportIndex, rtDisplaySet, rtIsLoading]); + + useEffect(() => { + const { unsubscribe } = segmentationService.subscribe( + segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE, + evt => { + if ( + evt.rtDisplaySet.displaySetInstanceUID === + rtDisplaySet.displaySetInstanceUID + ) { + setRtIsLoading(false); + } + + if (evt.overlappingSegments) { + uiNotificationService.show({ + title: 'Overlapping Segments', + message: + 'Overlapping segments detected which is not currently supported', + type: 'warning', + }); + } + } + ); + + return () => { + unsubscribe(); + }; + }, [rtDisplaySet]); + + useEffect(() => { + const { unsubscribe } = segmentationService.subscribe( + segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE, + ({ percentComplete, numSegments }) => { + setProcessingProgress({ + percentComplete, + totalSegments: numSegments, + }); + } + ); + + return () => { + unsubscribe(); + }; + }, [rtDisplaySet]); + + /** + Cleanup the SEG viewport when the viewport is destroyed + */ + useEffect(() => { + const onDisplaySetsRemovedSubscription = displaySetService.subscribe( + displaySetService.EVENTS.DISPLAY_SETS_REMOVED, + ({ displaySetInstanceUIDs }) => { + const activeViewport = viewports[activeViewportIndex]; + if ( + displaySetInstanceUIDs.includes(activeViewport.displaySetInstanceUID) + ) { + viewportGridService.setDisplaySetsForViewport({ + viewportIndex: activeViewportIndex, + displaySetInstanceUIDs: [], + }); + } + } + ); + + return () => { + onDisplaySetsRemovedSubscription.unsubscribe(); + }; + }, []); + + useEffect(() => { + let toolGroup = toolGroupService.getToolGroup(toolGroupId); + + if (toolGroup) { + return; + } + + toolGroup = createRTToolGroupAndAddTools( + toolGroupService, + customizationService, + toolGroupId + ); + + setToolGroupCreated(true); + + return () => { + // remove the segmentation representations if seg displayset changed + segmentationService.removeSegmentationRepresentationFromToolGroup( + toolGroupId + ); + + toolGroupService.destroyToolGroup(toolGroupId); + }; + }, []); + + useEffect(() => { + setIsHydrated(rtDisplaySet.isHydrated); + + return () => { + // remove the segmentation representations if seg displayset changed + segmentationService.removeSegmentationRepresentationFromToolGroup( + toolGroupId + ); + referencedDisplaySetRef.current = null; + }; + }, [rtDisplaySet]); + + // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + let childrenWithProps = null; + + if ( + !referencedDisplaySetRef.current || + referencedDisplaySet.displaySetInstanceUID !== + referencedDisplaySetRef.current.displaySet.displaySetInstanceUID + ) { + return null; + } + + if (children && children.length) { + childrenWithProps = children.map((child, index) => { + return ( + child && + React.cloneElement(child, { + viewportIndex, + key: index, + }) + ); + }); + } + + const { + PatientID, + PatientName, + PatientSex, + PatientAge, + SliceThickness, + ManufacturerModelName, + StudyDate, + SeriesDescription, + SpacingBetweenSlices, + SeriesNumber, + } = referencedDisplaySetRef.current.metadata; + + const onStatusClick = async () => { + const isHydrated = await _hydrateRTDisplaySet({ + rtDisplaySet, + viewportIndex, + servicesManager, + }); + + setIsHydrated(isHydrated); + }; + + return ( + <> + { + evt.stopPropagation(); + evt.preventDefault(); + }} + onArrowsClick={onSegmentChange} + getStatusComponent={() => { + return _getStatusComponent({ + isHydrated, + onStatusClick, + }); + }} + studyData={{ + label: viewportLabel, + useAltStyling: true, + studyDate: formatDate(StudyDate), + currentSeries: SeriesNumber, + seriesDescription: `RT Viewport ${SeriesDescription}`, + patientInformation: { + patientName: PatientName + ? OHIF.utils.formatPN(PatientName.Alphabetic) + : '', + patientSex: PatientSex || '', + patientAge: PatientAge || '', + MRN: PatientID || '', + thickness: SliceThickness ? `${SliceThickness.toFixed(2)}mm` : '', + spacing: + SpacingBetweenSlices !== undefined + ? `${SpacingBetweenSlices.toFixed(2)}mm` + : '', + scanner: ManufacturerModelName || '', + }, + }} + /> + +
+ {rtIsLoading && ( + + )} + {getCornerstoneViewport()} +
+ {viewportDialogState.viewportIndex === viewportIndex && ( + + )} +
+ {childrenWithProps} +
+ + ); +} + +OHIFCornerstoneRTViewport.propTypes = { + displaySets: PropTypes.arrayOf(PropTypes.object), + viewportIndex: PropTypes.number.isRequired, + dataSource: PropTypes.object, + children: PropTypes.node, + customProps: PropTypes.object, +}; + +OHIFCornerstoneRTViewport.defaultProps = { + customProps: {}, +}; + +function _getReferencedDisplaySetMetadata(referencedDisplaySet) { + const image0 = referencedDisplaySet.images[0]; + const referencedDisplaySetMetadata = { + PatientID: image0.PatientID, + PatientName: image0.PatientName, + PatientSex: image0.PatientSex, + PatientAge: image0.PatientAge, + SliceThickness: image0.SliceThickness, + StudyDate: image0.StudyDate, + SeriesDescription: image0.SeriesDescription, + SeriesInstanceUID: image0.SeriesInstanceUID, + SeriesNumber: image0.SeriesNumber, + ManufacturerModelName: image0.ManufacturerModelName, + SpacingBetweenSlices: image0.SpacingBetweenSlices, + }; + + return referencedDisplaySetMetadata; +} + +export default OHIFCornerstoneRTViewport; diff --git a/extensions/cornerstone-dicom-rt/src/viewports/_getStatusComponent.tsx b/extensions/cornerstone-dicom-rt/src/viewports/_getStatusComponent.tsx new file mode 100644 index 000000000..fee3d619a --- /dev/null +++ b/extensions/cornerstone-dicom-rt/src/viewports/_getStatusComponent.tsx @@ -0,0 +1,54 @@ +import React from 'react'; +import { useTranslation } from 'react-i18next'; +import { Icon, Tooltip } from '@ohif/ui'; + +export default function _getStatusComponent({ isHydrated, onStatusClick }) { + let ToolTipMessage = null; + let StatusIcon = null; + + const { t } = useTranslation('Common'); + const loadStr = t('LOAD'); + + switch (isHydrated) { + case true: + StatusIcon = () => ; + + ToolTipMessage = () => ( +
This Segmentation is loaded in the segmentation panel
+ ); + break; + case false: + StatusIcon = () => ; + + ToolTipMessage = () =>
Click LOAD to load RTSTRUCT.
; + } + + const StatusArea = () => ( +
+
+ + RTSTRUCT +
+ {!isHydrated && ( +
+ {loadStr} +
+ )} +
+ ); + + return ( + <> + {ToolTipMessage && ( + } position="bottom-left"> + + + )} + {!ToolTipMessage && } + + ); +} diff --git a/extensions/cornerstone-dicom-seg/LICENSE b/extensions/cornerstone-dicom-seg/LICENSE index 898d93d0b..983c5ef34 100644 --- a/extensions/cornerstone-dicom-seg/LICENSE +++ b/extensions/cornerstone-dicom-seg/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2022 Open Health Imaging Foundation +Copyright (c) 2023 Open Health Imaging Foundation Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in diff --git a/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js b/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js index de9212d84..b92da5382 100644 --- a/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js +++ b/extensions/cornerstone-dicom-seg/src/getSopClassHandlerModule.js @@ -57,6 +57,7 @@ function _getDisplaySetsFromSeries( wadoRoot, wadoUriRoot, wadoUri, + isOverlayDisplaySet: true, }; const referencedSeriesSequence = instance.ReferencedSeriesSequence; @@ -102,9 +103,12 @@ function _getDisplaySetsFromSeries( function _load(segDisplaySet, servicesManager, extensionManager, headers) { const { SOPInstanceUID } = segDisplaySet; + const { segmentationService } = servicesManager.services; + if ( (segDisplaySet.loading || segDisplaySet.isLoaded) && - loadPromises[SOPInstanceUID] + loadPromises[SOPInstanceUID] && + _segmentationExists(segDisplaySet, segmentationService) ) { return loadPromises[SOPInstanceUID]; } @@ -114,12 +118,6 @@ function _load(segDisplaySet, servicesManager, extensionManager, headers) { // We don't want to fire multiple loads, so we'll wait for the first to finish // and also return the same promise to any other callers. loadPromises[SOPInstanceUID] = new Promise(async (resolve, reject) => { - const { segmentationService } = servicesManager.services; - - if (_segmentationExistsInCache(segDisplaySet, segmentationService)) { - return; - } - if ( !segDisplaySet.segments || Object.keys(segDisplaySet.segments).length === 0 @@ -134,11 +132,8 @@ function _load(segDisplaySet, servicesManager, extensionManager, headers) { } const suppressEvents = true; - segmentationService.createSegmentationForSEGDisplaySet( - segDisplaySet, - null, - suppressEvents - ) + segmentationService + .createSegmentationForSEGDisplaySet(segDisplaySet, null, suppressEvents) .then(() => { segDisplaySet.loading = false; resolve(); @@ -176,12 +171,11 @@ async function _loadSegments(extensionManager, segDisplaySet, headers) { return segments; } -function _segmentationExistsInCache(segDisplaySet, segmentationService) { +function _segmentationExists(segDisplaySet, segmentationService) { // This should be abstracted with the CornerstoneCacheService - const labelmapVolumeId = segDisplaySet.displaySetInstanceUID; - const segVolume = segmentationService.getLabelmapVolume(labelmapVolumeId); - - return segVolume !== undefined; + return segmentationService.getSegmentation( + segDisplaySet.displaySetInstanceUID + ); } function _getPixelData(dataset, segments) { diff --git a/extensions/cornerstone-dicom-seg/src/index.tsx b/extensions/cornerstone-dicom-seg/src/index.tsx index 22a6ec491..54dff2255 100644 --- a/extensions/cornerstone-dicom-seg/src/index.tsx +++ b/extensions/cornerstone-dicom-seg/src/index.tsx @@ -3,7 +3,9 @@ import React from 'react'; import { Types } from '@ohif/core'; -import getSopClassHandlerModule, { protocols } from './getSopClassHandlerModule'; +import getSopClassHandlerModule, { + protocols, +} from './getSopClassHandlerModule'; import PanelSegmentation from './panels/PanelSegmentation'; import getHangingProtocolModule from './getHangingProtocolModule'; @@ -31,13 +33,17 @@ const extension = { */ id, - /** + /** * PanelModule should provide a list of panels that will be available in OHIF * for Modes to consume and render. Each panel is defined by a {name, * iconName, iconLabel, label, component} object. Example of a panel module * is the StudyBrowserPanel that is provided by the default extension in OHIF. */ - getPanelModule: ({ servicesManager, commandsManager, extensionManager }: Types.Extensions.ExtensionParams): Types.Panel[] => { + getPanelModule: ({ + servicesManager, + commandsManager, + extensionManager, + }): Types.Panel[] => { const wrappedPanelSegmentation = () => { return ( segmentationService.getSegmentations() @@ -62,6 +55,7 @@ export default function PanelSegmentation({ const { unsubscribe } = segmentationService.subscribe(evt, () => { const segmentations = segmentationService.getSegmentations(); setSegmentations(segmentations); + setSegmentationConfiguration(segmentationService.getConfiguration()); }); subscriptions.push(unsubscribe); }); @@ -184,7 +178,7 @@ export default function PanelSegmentation({ segmentationService.toggleSegmentationVisibility(segmentationId); }; - const setSegmentationConfiguration = useCallback( + const _setSegmentationConfiguration = useCallback( (segmentationId, key, value) => { segmentationService.setConfiguration({ segmentationId, @@ -214,54 +208,51 @@ export default function PanelSegmentation({ onToggleSegmentVisibility={onToggleSegmentVisibility} onToggleSegmentationVisibility={onToggleSegmentationVisibility} onToggleMinimizeSegmentation={onToggleMinimizeSegmentation} - segmentationConfig={{ - initialConfig: initialSegmentationConfigurations, - usePercentage: true, - }} + segmentationConfig={{ initialConfig: segmentationConfiguration }} setRenderOutline={value => - setSegmentationConfiguration( + _setSegmentationConfiguration( selectedSegmentationId, 'renderOutline', value ) } setOutlineOpacityActive={value => - setSegmentationConfiguration( + _setSegmentationConfiguration( selectedSegmentationId, 'outlineOpacity', value ) } setRenderFill={value => - setSegmentationConfiguration( + _setSegmentationConfiguration( selectedSegmentationId, 'renderFill', value ) } setRenderInactiveSegmentations={value => - setSegmentationConfiguration( + _setSegmentationConfiguration( selectedSegmentationId, 'renderInactiveSegmentations', value ) } setOutlineWidthActive={value => - setSegmentationConfiguration( + _setSegmentationConfiguration( selectedSegmentationId, 'outlineWidthActive', value ) } setFillAlpha={value => - setSegmentationConfiguration( + _setSegmentationConfiguration( selectedSegmentationId, 'fillAlpha', value ) } setFillAlphaInactive={value => - setSegmentationConfiguration( + _setSegmentationConfiguration( selectedSegmentationId, 'fillAlphaInactive', value diff --git a/extensions/cornerstone-dicom-seg/src/panels/segmentationConfigReducer.tsx b/extensions/cornerstone-dicom-seg/src/panels/segmentationConfigReducer.tsx index 0fbf58b2a..02857e86b 100644 --- a/extensions/cornerstone-dicom-seg/src/panels/segmentationConfigReducer.tsx +++ b/extensions/cornerstone-dicom-seg/src/panels/segmentationConfigReducer.tsx @@ -1,5 +1,3 @@ -import React, { useReducer } from 'react'; - // Todo: use defaults in cs3d const initialState = { renderOutline: true, diff --git a/extensions/cornerstone-dicom-seg/src/utils/initSEGToolGroup.ts b/extensions/cornerstone-dicom-seg/src/utils/initSEGToolGroup.ts index fe114dbcd..e032542f1 100644 --- a/extensions/cornerstone-dicom-seg/src/utils/initSEGToolGroup.ts +++ b/extensions/cornerstone-dicom-seg/src/utils/initSEGToolGroup.ts @@ -1,34 +1,12 @@ function createSEGToolGroupAndAddTools( - toolGroupService, - toolGroupId, - extensionManager + ToolGroupService, + customizationService, + toolGroupId ) { - const utilityModule = extensionManager.getModuleEntry( - '@ohif/extension-cornerstone.utilityModule.tools' - ); + const { tools } = + customizationService.get('cornerstone.overlayViewportTools') ?? {}; - const { toolNames, Enums } = utilityModule.exports; - - const tools = { - active: [ - { - toolName: toolNames.WindowLevel, - bindings: [{ mouseButton: Enums.MouseBindings.Primary }], - }, - { - toolName: toolNames.Pan, - bindings: [{ mouseButton: Enums.MouseBindings.Auxiliary }], - }, - { - toolName: toolNames.Zoom, - bindings: [{ mouseButton: Enums.MouseBindings.Secondary }], - }, - { toolName: toolNames.StackScrollMouseWheel, bindings: [] }, - ], - enabled: [{ toolName: toolNames.SegmentationDisplay }], - }; - - return toolGroupService.createToolGroupAndAddTools(toolGroupId, tools, {}); + return ToolGroupService.createToolGroupAndAddTools(toolGroupId, tools, {}); } export default createSEGToolGroupAndAddTools; diff --git a/extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx b/extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx index f16df5f6b..e901ac0be 100644 --- a/extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx +++ b/extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx @@ -3,7 +3,11 @@ import React, { useCallback, useEffect, useRef, useState } from 'react'; import { useTranslation } from 'react-i18next'; import OHIF, { utils } from '@ohif/core'; import { - LoadingIndicatorProgress, Notification, useViewportDialog, useViewportGrid, ViewportActionBar + LoadingIndicatorTotalPercent, + Notification, + useViewportDialog, + useViewportGrid, + ViewportActionBar, } from '@ohif/ui'; import createSEGToolGroupAndAddTools from '../utils/initSEGToolGroup'; import promptHydrateSEG from '../utils/promptHydrateSEG'; @@ -31,6 +35,7 @@ function OHIFCornerstoneSEGViewport(props) { toolGroupService, segmentationService, uiNotificationService, + customizationService, } = servicesManager.services; const toolGroupId = `${SEG_TOOLGROUP_BASE_NAME}-${viewportIndex}`; @@ -58,7 +63,7 @@ function OHIFCornerstoneSEGViewport(props) { const [segIsLoading, setSegIsLoading] = useState(!segDisplaySet.isLoaded); const [element, setElement] = useState(null); const [processingProgress, setProcessingProgress] = useState({ - segmentIndex: 1, + percentComplete: null, totalSegments: null, }); @@ -129,6 +134,8 @@ function OHIFCornerstoneSEGViewport(props) { let newSelectedSegmentIndex = selectedSegment + direction; + // Segment 0 is always background + if (newSelectedSegmentIndex > numberOfSegments - 1) { newSelectedSegmentIndex = 1; } else if (newSelectedSegmentIndex === 0) { @@ -163,7 +170,7 @@ function OHIFCornerstoneSEGViewport(props) { useEffect(() => { const { unsubscribe } = segmentationService.subscribe( - segmentationService.EVENTS.SEGMENTATION_PIXEL_DATA_CREATED, + segmentationService.EVENTS.SEGMENTATION_LOADING_COMPLETE, evt => { if ( evt.segDisplaySet.displaySetInstanceUID === @@ -190,10 +197,10 @@ function OHIFCornerstoneSEGViewport(props) { useEffect(() => { const { unsubscribe } = segmentationService.subscribe( - segmentationService.EVENTS.SEGMENT_PIXEL_DATA_CREATED, - ({ segmentIndex, numSegments }) => { + segmentationService.EVENTS.SEGMENT_LOADING_COMPLETE, + ({ percentComplete, numSegments }) => { setProcessingProgress({ - segmentIndex, + percentComplete, totalSegments: numSegments, }); } @@ -239,8 +246,8 @@ function OHIFCornerstoneSEGViewport(props) { // only, and does NOT interfere with currently displayed segmentations. toolGroup = createSEGToolGroupAndAddTools( toolGroupService, - toolGroupId, - extensionManager + customizationService, + toolGroupId ); setToolGroupCreated(true); @@ -351,27 +358,11 @@ function OHIFCornerstoneSEGViewport(props) {
{segIsLoading && ( - Loading SEG ... - ) : ( - -
Loading Segment
-
{`${processingProgress.segmentIndex}`}
-
/
-
{`${processingProgress.totalSegments}`}
- - ) - } + totalNumbers={processingProgress.totalSegments} + percentComplete={processingProgress.percentComplete} + loadingText="Loading SEG..." /> )} {getCornerstoneViewport()} diff --git a/extensions/cornerstone-dicom-sr/package.json b/extensions/cornerstone-dicom-sr/package.json index 2dc6b9edc..34aa3e523 100644 --- a/extensions/cornerstone-dicom-sr/package.json +++ b/extensions/cornerstone-dicom-sr/package.json @@ -47,6 +47,6 @@ "classnames": "^2.3.2", "@cornerstonejs/adapters": "^0.6.0", "@cornerstonejs/core": "^0.42.2", - "@cornerstonejs/tools": "^0.61.11" + "@cornerstonejs/tools": "^0.63.2" } } diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json index 526074be1..d6a6a3ee1 100644 --- a/extensions/cornerstone/package.json +++ b/extensions/cornerstone/package.json @@ -50,8 +50,8 @@ "@babel/runtime": "^7.20.13", "@cornerstonejs/adapters": "^0.6.0", "@cornerstonejs/core": "^0.42.2", - "@cornerstonejs/streaming-image-volume-loader": "^0.16.0", - "@cornerstonejs/tools": "^0.61.11", + "@cornerstonejs/streaming-image-volume-loader": "^0.16.2", + "@cornerstonejs/tools": "^0.63.2", "@kitware/vtk.js": "26.5.6", "html2canvas": "^1.4.1", "lodash.debounce": "4.0.8", diff --git a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx index f3e061900..d74a3b99b 100644 --- a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx +++ b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx @@ -630,19 +630,19 @@ function _jumpToMeasurement( } else { // for volume viewport we can't rely on the imageIdIndex since it can be // a reconstructed view that doesn't match the original slice numbers etc. - const { viewPlaneNormal } = measurement.metadata; + const { viewPlaneNormal: measurementViewPlane } = measurement.metadata; imageIdIndex = referencedDisplaySet.images.findIndex( i => i.SOPInstanceUID === SOPInstanceUID ); - const { orientation } = viewportInfo.getViewportOptions(); + const { viewPlaneNormal: viewportViewPlane } = viewport.getCamera(); + // should compare abs for both planes since the direction can be flipped if ( - orientation && - viewPlaneNormal && + measurementViewPlane && !csUtils.isEqual( - CONSTANTS.MPR_CAMERA_VALUES[orientation]?.viewPlaneNormal, - viewPlaneNormal + measurementViewPlane.map(Math.abs), + viewportViewPlane.map(Math.abs) ) ) { viewportCameraDirectionMatch = false; diff --git a/extensions/cornerstone/src/getCustomizationModule.ts b/extensions/cornerstone/src/getCustomizationModule.ts new file mode 100644 index 000000000..fa548b74a --- /dev/null +++ b/extensions/cornerstone/src/getCustomizationModule.ts @@ -0,0 +1,37 @@ +import { Enums } from '@cornerstonejs/tools'; +import { toolNames } from './initCornerstoneTools'; + +const tools = { + active: [ + { + toolName: toolNames.WindowLevel, + bindings: [{ mouseButton: Enums.MouseBindings.Primary }], + }, + { + toolName: toolNames.Pan, + bindings: [{ mouseButton: Enums.MouseBindings.Auxiliary }], + }, + { + toolName: toolNames.Zoom, + bindings: [{ mouseButton: Enums.MouseBindings.Secondary }], + }, + { toolName: toolNames.StackScrollMouseWheel, bindings: [] }, + ], + enabled: [{ toolName: toolNames.SegmentationDisplay }], +}; + +function getCustomizationModule() { + return [ + { + name: 'default', + value: [ + { + id: 'cornerstone.overlayViewportTools', + tools, + }, + ], + }, + ]; +} + +export default getCustomizationModule; diff --git a/extensions/cornerstone/src/index.tsx b/extensions/cornerstone/src/index.tsx index 29387df19..643022e15 100644 --- a/extensions/cornerstone/src/index.tsx +++ b/extensions/cornerstone/src/index.tsx @@ -10,6 +10,7 @@ import { Enums as cs3DToolsEnums } from '@cornerstonejs/tools'; import { ServicesManager, Types } from '@ohif/core'; import init from './init'; +import getCustomizationModule from './getCustomizationModule'; import getCommandsModule from './commandsModule'; import getHangingProtocolModule from './getHangingProtocolModule'; import ToolGroupService from './services/ToolGroupService'; @@ -108,6 +109,7 @@ const cornerstoneExtension: Types.Extensions.Extension = { ]; }, getCommandsModule, + getCustomizationModule, getUtilityModule({ servicesManager }) { return [ { @@ -139,5 +141,5 @@ const cornerstoneExtension: Types.Extensions.Extension = { }; export type { PublicViewportOptions }; -export { measurementMappingUtils, CornerstoneExtensionTypes }; +export { measurementMappingUtils, CornerstoneExtensionTypes, toolNames }; export default cornerstoneExtension; diff --git a/extensions/cornerstone/src/init.tsx b/extensions/cornerstone/src/init.tsx index 27ca02ee7..377cbbe82 100644 --- a/extensions/cornerstone/src/init.tsx +++ b/extensions/cornerstone/src/init.tsx @@ -1,4 +1,4 @@ -import OHIF from '@ohif/core'; +import OHIF, { Types } from '@ohif/core'; import React from 'react'; import * as cornerstone from '@cornerstonejs/core'; diff --git a/extensions/cornerstone/src/services/SegmentationService/RTSTRUCT/mapROIContoursToRTStructData.ts b/extensions/cornerstone/src/services/SegmentationService/RTSTRUCT/mapROIContoursToRTStructData.ts new file mode 100644 index 000000000..f17ec5c70 --- /dev/null +++ b/extensions/cornerstone/src/services/SegmentationService/RTSTRUCT/mapROIContoursToRTStructData.ts @@ -0,0 +1,38 @@ +/** + * Maps a DICOM RT Struct ROI Contour to a RTStruct data that can be used + * in Segmentation Service + * + * @param structureSet - A DICOM RT Struct ROI Contour + * @param rtDisplaySetUID - A CornerstoneTools DisplaySet UID + * @returns An array of object that includes data, id, segmentIndex, color + * and geometry Id + */ +export function mapROIContoursToRTStructData( + structureSet: unknown, + rtDisplaySetUID: unknown +) { + return structureSet.ROIContours.map( + ({ contourPoints, ROINumber, ROIName, colorArray }) => { + const data = contourPoints.map(({ points, ...rest }) => { + const newPoints = points.map(({ x, y, z }) => { + return [x, y, z]; + }); + + return { + ...rest, + points: newPoints, + }; + }); + + const id = ROIName || ROINumber; + + return { + data, + id, + segmentIndex: ROINumber, + color: colorArray, + geometryId: `${rtDisplaySetUID}:${id}:segmentIndex-${ROINumber}`, + }; + } + ); +} diff --git a/extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts b/extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts index d4c25bee4..b9882e3ed 100644 --- a/extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts +++ b/extensions/cornerstone/src/services/SegmentationService/SegmentationService.ts @@ -3,10 +3,11 @@ import cloneDeep from 'lodash.clonedeep'; import { Types as OhifTypes, ServicesManager, PubSubService } from '@ohif/core'; import { cache, + Enums as csEnums, + geometryLoader, eventTarget, getEnabledElementByIds, metaData, - Types, utilities as csUtils, volumeLoader, } from '@cornerstonejs/core'; @@ -18,15 +19,18 @@ import { utilities as cstUtils, } from '@cornerstonejs/tools'; import isEqual from 'lodash.isequal'; -import { easeInOutBell } from '../../utils/transitions'; +import { Types as ohifTypes } from '@ohif/core'; +import { easeInOutBell, reverseEaseInOutBell } from '../../utils/transitions'; import { + Segment, Segmentation, SegmentationConfig, - SegmentationSchema, } from './SegmentationServiceTypes'; +import { mapROIContoursToRTStructData } from './RTSTRUCT/mapROIContoursToRTStructData'; const { COLOR_LUT } = cstConstants; const LABELMAP = csToolsEnums.SegmentationRepresentations.Labelmap; +const CONTOUR = csToolsEnums.SegmentationRepresentations.Contour; const EVENTS = { // fired when the segmentation is updated (e.g. when a segment is added, removed, or modified, locked, visibility changed etc.) @@ -40,13 +44,22 @@ const EVENTS = { // fired when the configuration for the segmentation is changed (e.g., brush size, render fill, outline thickness, etc.) SEGMENTATION_CONFIGURATION_CHANGED: 'event::segmentation_configuration_changed', - SEGMENT_PIXEL_DATA_CREATED: 'event::segment_pixel_data_created', + // fired when the active segment is loaded in SEG or RTSTRUCT + SEGMENT_LOADING_COMPLETE: 'event::segment_loading_complete', // for all segments - SEGMENTATION_PIXEL_DATA_CREATED: 'event::segmentation_pixel_data_created', + SEGMENTATION_LOADING_COMPLETE: 'event::segmentation_loading_complete', }; const VALUE_TYPES = {}; +const SEGMENT_CONSTANT = { + opacity: 255, + isVisible: true, + isLocked: false, +}; + +const VOLUME_LOADER_SCHEME = 'cornerstoneStreamingImageVolume'; + class SegmentationService extends PubSubService { static REGISTRATION = { name: 'segmentationService', @@ -75,7 +88,7 @@ class SegmentationService extends PubSubService { public destroy = () => { eventTarget.removeEventListener( csToolsEnums.Events.SEGMENTATION_MODIFIED, - this._onSegmentationModified + this._onSegmentationModifiedFromSource ); eventTarget.removeEventListener( @@ -112,7 +125,7 @@ class SegmentationService extends PubSubService { toolGroupId?: string, properties?: { label?: string; - color?: Types.Point3; + color?: ohifTypes.RGB; opacity?: number; visibility?: boolean; isLocked?: boolean; @@ -239,7 +252,8 @@ class SegmentationService extends PubSubService { // Todo: handle other segmentations other than labelmap const labelmapVolume = this.getLabelmapVolume(segmentationId); - const { scalarData, dimensions } = labelmapVolume; + const { dimensions } = labelmapVolume; + const scalarData = labelmapVolume.getScalarData(); // Set all values of this segment to zero and get which frames have been edited. const frameLength = dimensions[0] * dimensions[1]; @@ -324,7 +338,7 @@ class SegmentationService extends PubSubService { public setSegmentColor( segmentationId: string, segmentIndex: number, - color: Types.Point3, + color: ohifTypes.RGB, toolGroupId?: string ): void { this._setSegmentColor(segmentationId, segmentIndex, color, toolGroupId); @@ -438,15 +452,15 @@ class SegmentationService extends PubSubService { } public addOrUpdateSegmentation( - segmentationSchema: SegmentationSchema, + segmentation: Segmentation, suppressEvents = false, notYetUpdatedAtSource = false ): string { - const { id: segmentationId } = segmentationSchema; - let segmentation = this.segmentations[segmentationId]; - if (segmentation) { + const { id: segmentationId } = segmentation; + let cachedSegmentation = this.segmentations[segmentationId]; + if (cachedSegmentation) { // Update the segmentation (mostly for assigning metadata/labels) - Object.assign(segmentation, segmentationSchema); + Object.assign(cachedSegmentation, segmentation); this._updateCornerstoneSegmentations({ segmentationId, @@ -455,53 +469,47 @@ class SegmentationService extends PubSubService { if (!suppressEvents) { this._broadcastEvent(this.EVENTS.SEGMENTATION_UPDATED, { - segmentation, + segmentation: cachedSegmentation, }); } return segmentationId; } - // Add the segmentation otherwise + const representationType = segmentation.type; + const representationData = + segmentation.representationData[representationType]; cstSegmentation.addSegmentations([ { segmentationId, representation: { - type: LABELMAP, - // Todo: need to be generalized + type: representationType, data: { - volumeId: segmentationId, + ...representationData, }, }, }, ]); // Define a new color LUT and associate it with this segmentation. - // Todo: need to be generalized to accept custom color LUTs const newColorLUT = this.generateNewColorLUT(); const newColorLUTIndex = this.getNextColorLUTIndex(); cstSegmentation.config.color.addColorLUT(newColorLUT, newColorLUTIndex); - if ( - segmentationSchema.label === undefined || - segmentationSchema.label === '' - ) { - segmentationSchema.label = 'Segmentation'; - } - this.segmentations[segmentationId] = { - ...segmentationSchema, - segments: segmentationSchema.segments || [null], - activeSegmentIndex: segmentationSchema.activeSegmentIndex ?? null, - segmentCount: segmentationSchema.segmentCount ?? 0, + ...segmentation, + label: segmentation.label || '', + segments: segmentation.segments || [null], + activeSegmentIndex: segmentation.activeSegmentIndex ?? null, + segmentCount: segmentation.segmentCount ?? 0, isActive: false, colorLUTIndex: newColorLUTIndex, isVisible: true, }; - segmentation = this.segmentations[segmentationId]; + cachedSegmentation = this.segmentations[segmentationId]; this._updateCornerstoneSegmentations({ segmentationId, @@ -510,11 +518,11 @@ class SegmentationService extends PubSubService { if (!suppressEvents) { this._broadcastEvent(this.EVENTS.SEGMENTATION_ADDED, { - segmentation, + segmentation: cachedSegmentation, }); } - return segmentation.id; + return cachedSegmentation.id; } public async createSegmentationForSEGDisplaySet( @@ -522,7 +530,38 @@ class SegmentationService extends PubSubService { segmentationId?: string, suppressEvents = false ): Promise { + // Todo: we only support creating labelmap for SEG displaySets for now + const representationType = LABELMAP; + segmentationId = segmentationId ?? segDisplaySet.displaySetInstanceUID; + + const defaultScheme = this._getDefaultSegmentationScheme(); + + const segmentation: Segmentation = { + ...defaultScheme, + id: segmentationId, + displaySetInstanceUID: segDisplaySet.displaySetInstanceUID, + type: representationType, + representationData: { + [LABELMAP]: { + volumeId: segmentationId, + referencedVolumeId: segDisplaySet.referencedVolumeId, + }, + }, + }; + + const labelmap = this.getLabelmapVolume(segmentationId); + const cachedSegmentation = this.getSegmentation(segmentationId); + if (labelmap && cachedSegmentation) { + // if the labelmap with the same segmentationId already exists, we can + // just assume that the segmentation is already created and move on with + // updating the state + return this.addOrUpdateSegmentation( + Object.assign(segmentation, cachedSegmentation), + suppressEvents + ); + } + const { segments, referencedVolumeId } = segDisplaySet; if (!segments || !referencedVolumeId) { @@ -531,38 +570,8 @@ class SegmentationService extends PubSubService { ); } - const segmentationSchema: SegmentationSchema = { - id: segmentationId, - volumeId: segmentationId, - displaySetInstanceUID: segDisplaySet.displaySetInstanceUID, - referencedVolumeURI: segDisplaySet.referencedVolumeURI, - activeSegmentIndex: 1, - cachedStats: {}, - label: '', - segmentsLocked: [], - type: LABELMAP, - displayText: [], - hydrated: false, // by default we don't hydrate the segmentation for SEG displaySets - segmentCount: 0, - segments: [], - }; - - const labelmap = this.getLabelmapVolume(segmentationId); - const segmentation = this.getSegmentation(segmentationId); - - if (labelmap && segmentation) { - // if the labalemap with the same segmentationId already exists, we can - // just assume that the segmentation is already created and move on with - // updating the state - return this.addOrUpdateSegmentation( - Object.assign(segmentationSchema, segmentation), - suppressEvents - ); - } - // if the labelmap doesn't exist, we need to create it first from the // DICOM SEG displaySet data - const referencedVolume = cache.getVolume(referencedVolumeId); if (!referencedVolume) { @@ -584,7 +593,7 @@ class SegmentationService extends PubSubService { } ); const [rows, columns] = derivedVolume.dimensions; - const derivedVolumeScalarData = derivedVolume.scalarData; + const derivedVolumeScalarData = derivedVolume.getScalarData(); const { imageIds } = referencedVolume; const sopUIDImageIdIndexMap = imageIds.reduce((acc, imageId, index) => { @@ -667,26 +676,34 @@ class SegmentationService extends PubSubService { const centerWorld = derivedVolume.imageData.indexToWorld([x, y, z]); - segmentationSchema.cachedStats = { - ...segmentationSchema.cachedStats, + segmentation.cachedStats = { + ...segmentation.cachedStats, segmentCenter: { - ...segmentationSchema.cachedStats.segmentCenter, + ...segmentation.cachedStats.segmentCenter, [segmentIndex]: { center: { image: [x, y, z], world: centerWorld, }, - modifiedTime: Date.now(), + modifiedTime: segDisplaySet.SeriesDate, }, }, }; - this._broadcastEvent(EVENTS.SEGMENT_PIXEL_DATA_CREATED, { - segmentIndex: Number(segmentIndex), - numSegments, + const numInitialized = Object.keys(segmentation.cachedStats.segmentCenter) + .length; + + // Calculate percentage completed + const percentComplete = Math.round((numInitialized / numSegments) * 100); + + this._broadcastEvent(EVENTS.SEGMENT_LOADING_COMPLETE, { + percentComplete, + numSegments: numSegments, }); }; + const promiseArray = []; + for (const segmentIndex in segments) { const segmentInfo = segments[segmentIndex]; @@ -700,17 +717,19 @@ class SegmentationService extends PubSubService { }, 0); }); - await promise; + promiseArray.push(promise); } - segmentationSchema.segmentCount = Object.keys(segments).length; - segmentationSchema.segments = [null]; // segment 0 + await Promise.all(promiseArray); + + segmentation.segmentCount = Object.keys(segments).length; + segmentation.segments = [null]; // segment 0 Object.keys(segments).forEach(segmentIndex => { const segmentInfo = segments[segmentIndex]; const segIndex = Number(segmentIndex); - segmentationSchema.segments[segIndex] = { + segmentation.segments[segIndex] = { label: segmentInfo.label || `Segment ${segIndex}`, segmentIndex: Number(segmentIndex), color: [ @@ -726,13 +745,151 @@ class SegmentationService extends PubSubService { segDisplaySet.isLoaded = true; - this._broadcastEvent(EVENTS.SEGMENTATION_PIXEL_DATA_CREATED, { + this._broadcastEvent(EVENTS.SEGMENTATION_LOADING_COMPLETE, { segmentationId, segDisplaySet, overlappingSegments, }); - return this.addOrUpdateSegmentation(segmentationSchema, suppressEvents); + return this.addOrUpdateSegmentation(segmentation, suppressEvents); + } + + public async createSegmentationForRTDisplaySet( + rtDisplaySet, + segmentationId?: string, + suppressEvents = false + ): Promise { + // Todo: we currently only have support for contour representation for initial + // RT display + const representationType = CONTOUR; + segmentationId = segmentationId ?? rtDisplaySet.displaySetInstanceUID; + const { structureSet } = rtDisplaySet; + + if (!structureSet) { + throw new Error( + 'To create the contours from RT displaySet, the displaySet should be loaded first, you can perform rtDisplaySet.load() before calling this method.' + ); + } + + const defaultScheme = this._getDefaultSegmentationScheme(); + const rtDisplaySetUID = rtDisplaySet.displaySetInstanceUID; + + const allRTStructData = mapROIContoursToRTStructData( + structureSet, + rtDisplaySetUID + ); + + // sort by segmentIndex + allRTStructData.sort((a, b) => a.segmentIndex - b.segmentIndex); + + const geometryIds = allRTStructData.map(({ geometryId }) => geometryId); + + const segmentation: Segmentation = { + ...defaultScheme, + id: segmentationId, + displaySetInstanceUID: rtDisplaySetUID, + type: representationType, + representationData: { + [CONTOUR]: { + geometryIds, + }, + }, + }; + + const cachedSegmentation = this.getSegmentation(segmentationId); + + if (cachedSegmentation) { + // if the labelmap with the same segmentationId already exists, we can + // just assume that the segmentation is already created and move on with + // updating the state + return this.addOrUpdateSegmentation( + Object.assign(segmentation, cachedSegmentation), + suppressEvents + ); + } + + if (!structureSet.ROIContours?.length) { + throw new Error( + 'The structureSet does not contain any ROIContours. Please ensure the structureSet is loaded first.' + ); + } + const segmentsCachedStats = {}; + const initializeContour = async rtStructData => { + const { data, id, color, segmentIndex, geometryId } = rtStructData; + const geometry = await geometryLoader.createAndCacheGeometry(geometryId, { + geometryData: { + data, + id, + color, + frameOfReferenceUID: structureSet.frameOfReferenceUID, + segmentIndex, + }, + type: csEnums.GeometryType.CONTOUR, + }); + + const contourSet = geometry.data; + const centroid = contourSet.getCentroid(); + + segmentsCachedStats[segmentIndex] = { + center: { world: centroid }, + modifiedTime: rtDisplaySet.SeriesDate, // we use the SeriesDate as the modifiedTime since this is the first time we are creating the segmentation + }; + + segmentation.segments[segmentIndex] = { + label: id, + segmentIndex, + color, + ...SEGMENT_CONSTANT, + }; + + const numInitialized = Object.keys(segmentsCachedStats).length; + + // Calculate percentage completed + const percentComplete = Math.round( + (numInitialized / allRTStructData.length) * 100 + ); + + this._broadcastEvent(EVENTS.SEGMENT_LOADING_COMPLETE, { + percentComplete, + // Note: this is not the geometryIds length since there might be + // some missing ROINumbers + numSegments: allRTStructData.length, + }); + }; + + const promiseArray = []; + + for (let i = 0; i < allRTStructData.length; i++) { + const promise = new Promise((resolve, reject) => { + setTimeout(() => { + initializeContour(allRTStructData[i]).then(() => { + resolve(); + }); + }, 0); + }); + + promiseArray.push(promise); + } + + await Promise.all(promiseArray); + + segmentation.segmentCount = allRTStructData.length; + rtDisplaySet.isLoaded = true; + + segmentation.cachedStats = { + ...segmentation.cachedStats, + segmentCenter: { + ...segmentation.cachedStats.segmentCenter, + ...segmentsCachedStats, + }, + }; + + this._broadcastEvent(EVENTS.SEGMENTATION_LOADING_COMPLETE, { + segmentationId, + rtDisplaySet, + }); + + return this.addOrUpdateSegmentation(segmentation, suppressEvents); } public jumpToSegmentCenter( @@ -743,7 +900,7 @@ class SegmentationService extends PubSubService { highlightSegment = true, animationLength = 750, highlightHideOthers = false, - highlightFunctionType: 'ease-in-out' // todo: make animation functions configurable from outside + highlightFunctionType = 'ease-in-out' // todo: make animation functions configurable from outside ): void { const { toolGroupService } = this.servicesManager.services; const center = this._getSegmentCenter(segmentationId, segmentIndex); @@ -797,7 +954,7 @@ class SegmentationService extends PubSubService { alpha = 0.9, animationLength = 750, hideOthers = true, - highlightFunctionType: 'ease-in-out' + highlightFunctionType = 'ease-in-out' ): void { if (this.highlightIntervalId) { clearInterval(this.highlightIntervalId); @@ -811,61 +968,25 @@ class SegmentationService extends PubSubService { toolGroupId ); + const { type } = segmentationRepresentation; const { segments } = segmentation; - const newSegmentSpecificConfig = { - [segmentIndex]: { - LABELMAP: { - fillAlpha: alpha, - }, - }, - }; + const highlightFn = + type === LABELMAP + ? this._highlightLabelmap.bind(this) + : this._highlightContour.bind(this); - if (hideOthers) { - for (let i = 0; i < segments.length; i++) { - if (i !== segmentIndex) { - newSegmentSpecificConfig[i] = { - LABELMAP: { - fillAlpha: 0, - }, - }; - } - } - } + const adjustedAlpha = type === LABELMAP ? alpha : 1 - alpha; - const { fillAlpha } = this.getConfiguration(toolGroupId); - - let count = 0; - const intervalTime = 16; - const numberOfFrames = Math.ceil(animationLength / intervalTime); - - this.highlightIntervalId = setInterval(() => { - const x = (count * intervalTime) / animationLength; - cstSegmentation.config.setSegmentSpecificConfig( - toolGroupId, - segmentationRepresentation.segmentationRepresentationUID, - { - [segmentIndex]: { - LABELMAP: { - fillAlpha: easeInOutBell(x, fillAlpha), - }, - }, - } - ); - - count++; - - if (count === numberOfFrames) { - clearInterval(this.highlightIntervalId); - cstSegmentation.config.setSegmentSpecificConfig( - toolGroupId, - segmentationRepresentation.segmentationRepresentationUID, - {} - ); - - this.highlightIntervalId = null; - } - }, intervalTime); + highlightFn( + segmentIndex, + adjustedAlpha, + hideOthers, + segments, + toolGroupId, + animationLength, + segmentationRepresentation + ); } public createSegmentationForDisplaySet = async ( @@ -875,8 +996,10 @@ class SegmentationService extends PubSubService { label: string; } ): Promise => { - const volumeLoaderScheme = 'cornerstoneStreamingImageVolume'; // Loader id which defines which volume loader to use - const volumeId = `${volumeLoaderScheme}:${displaySetInstanceUID}`; // VolumeId with loader id + volume id + // Todo: we currently only support labelmap for segmentation for a displaySet + const representationType = LABELMAP; + + const volumeId = this._getVolumeIdForDisplaySet(displaySetInstanceUID); const segmentationId = options?.segmentationId ?? `${csUtils.uuidv4()}`; @@ -890,23 +1013,25 @@ class SegmentationService extends PubSubService { }, }); - const segmentationSchema: SegmentationSchema = { + const defaultScheme = this._getDefaultSegmentationScheme(); + + const segmentation: Segmentation = { + ...defaultScheme, id: segmentationId, - volumeId: segmentationId, displaySetInstanceUID, - referencedVolumeURI: volumeId.split(':')[0], // Todo: this is so ugly - activeSegmentIndex: 1, - cachedStats: {}, label: options?.label, - segmentsLocked: [], - type: LABELMAP, - displayText: [], - hydrated: false, - segmentCount: 0, - segments: [], + // We should set it as active by default, as it created for display + isActive: true, + type: representationType, + representationData: { + LABELMAP: { + volumeId: segmentationId, + referencedVolumeId: volumeId, // Todo: this is so ugly + }, + }, }; - this.addOrUpdateSegmentation(segmentationSchema); + this.addOrUpdateSegmentation(segmentation); return segmentationId; }; @@ -1085,21 +1210,131 @@ class SegmentationService extends PubSubService { } }; + private _highlightLabelmap( + segmentIndex: number, + alpha: number, + hideOthers: boolean, + segments: Segment[], + toolGroupId: string, + animationLength: number, + segmentationRepresentation: cstTypes.ToolGroupSpecificRepresentation + ) { + const newSegmentSpecificConfig = { + [segmentIndex]: { + LABELMAP: { + fillAlpha: alpha, + }, + }, + }; + + if (hideOthers) { + for (let i = 0; i < segments.length; i++) { + if (i !== segmentIndex) { + newSegmentSpecificConfig[i] = { + LABELMAP: { + fillAlpha: 0, + }, + }; + } + } + } + + const { fillAlpha } = this.getConfiguration(toolGroupId); + + let count = 0; + const intervalTime = 16; + const numberOfFrames = Math.ceil(animationLength / intervalTime); + + this.highlightIntervalId = setInterval(() => { + const x = (count * intervalTime) / animationLength; + cstSegmentation.config.setSegmentSpecificConfig( + toolGroupId, + segmentationRepresentation.segmentationRepresentationUID, + { + [segmentIndex]: { + LABELMAP: { + fillAlpha: easeInOutBell(x, fillAlpha), + }, + }, + } + ); + + count++; + + if (count === numberOfFrames) { + clearInterval(this.highlightIntervalId); + cstSegmentation.config.setSegmentSpecificConfig( + toolGroupId, + segmentationRepresentation.segmentationRepresentationUID, + {} + ); + + this.highlightIntervalId = null; + } + }, intervalTime); + } + + private _highlightContour( + segmentIndex: number, + alpha: number, + hideOthers: boolean, + segments: Segment[], + toolGroupId: string, + animationLength: number, + segmentationRepresentation: cstTypes.ToolGroupSpecificRepresentation + ) { + const startTime = performance.now(); + + const animate = (currentTime: number) => { + const progress = (currentTime - startTime) / animationLength; + if (progress >= 1) { + cstSegmentation.config.setSegmentSpecificConfig( + toolGroupId, + segmentationRepresentation.segmentationRepresentationUID, + {} + ); + return; + } + + const reversedProgress = reverseEaseInOutBell(progress, 0.1); + cstSegmentation.config.setSegmentSpecificConfig( + toolGroupId, + segmentationRepresentation.segmentationRepresentationUID, + { + [segmentIndex]: { + CONTOUR: { + fillAlpha: reversedProgress, + }, + }, + } + ); + + requestAnimationFrame(animate); + }; + + requestAnimationFrame(animate); + } + public removeSegmentationRepresentationFromToolGroup( toolGroupId: string, - segmentationIds?: string[] + segmentationRepresentationUIDsIds?: string[] ): void { - segmentationIds = - segmentationIds ?? - cstSegmentation.state - .getSegmentationRepresentations(toolGroupId) - .map(rep => rep.segmentationRepresentationUID); + const uids = segmentationRepresentationUIDsIds || []; + if (!uids.length) { + const representations = cstSegmentation.state.getSegmentationRepresentations( + toolGroupId + ); - cstSegmentation.removeSegmentationsFromToolGroup( - toolGroupId, - segmentationIds, - true // immediate render - ); + if (!representations || !representations.length) { + return; + } + + uids.push( + ...representations.map(rep => rep.segmentationRepresentationUID) + ); + } + + cstSegmentation.removeSegmentationsFromToolGroup(toolGroupId, uids); } /** @@ -1162,10 +1397,16 @@ class SegmentationService extends PubSubService { // toolGroupId // ); + const segmentationRepresentations = this.getSegmentationRepresentationsForToolGroup( + toolGroupId + ); + + const typeToUse = segmentationRepresentations?.[0]?.type || LABELMAP; + const config = cstSegmentation.config.getGlobalConfig(); const { renderInactiveSegmentations } = config; - const labelmapRepresentationConfig = config.representations.LABELMAP; + const representation = config.representations[typeToUse]; const { renderOutline, @@ -1175,7 +1416,7 @@ class SegmentationService extends PubSubService { fillAlphaInactive, outlineOpacity, outlineOpacityInactive, - } = labelmapRepresentationConfig; + } = representation; return { brushSize, @@ -1204,48 +1445,33 @@ class SegmentationService extends PubSubService { renderOutline, } = configuration; - if (renderOutline !== undefined) { - this._setLabelmapConfigValue('renderOutline', renderOutline); - } + const setConfigValueIfDefined = (key, value, transformFn = null) => { + if (value !== undefined) { + const transformedValue = transformFn ? transformFn(value) : value; + this._setSegmentationConfig(key, transformedValue); + } + }; - if (outlineWidthActive !== undefined) { - this._setLabelmapConfigValue('outlineWidthActive', outlineWidthActive); - // this._setLabelmapConfigValue('outlineWidthInactive', outlineWidthActive); - } - - if (outlineOpacity !== undefined) { - this._setLabelmapConfigValue('outlineOpacity', outlineOpacity / 100); - } - - if (fillAlpha !== undefined) { - this._setLabelmapConfigValue('fillAlpha', fillAlpha / 100); - } - - if (renderFill !== undefined) { - this._setLabelmapConfigValue('renderFill', renderFill); - } + setConfigValueIfDefined('renderOutline', renderOutline); + setConfigValueIfDefined('outlineWidthActive', outlineWidthActive); + setConfigValueIfDefined('outlineOpacity', outlineOpacity, v => v / 100); + setConfigValueIfDefined('fillAlpha', fillAlpha, v => v / 100); + setConfigValueIfDefined('renderFill', renderFill); + setConfigValueIfDefined( + 'fillAlphaInactive', + fillAlphaInactive, + v => v / 100 + ); + setConfigValueIfDefined('outlineOpacityInactive', fillAlphaInactive, v => + Math.max(0.75, v / 100) + ); if (renderInactiveSegmentations !== undefined) { const config = cstSegmentation.config.getGlobalConfig(); - config.renderInactiveSegmentations = renderInactiveSegmentations; cstSegmentation.config.setGlobalConfig(config); } - if (fillAlphaInactive !== undefined) { - this._setLabelmapConfigValue( - 'fillAlphaInactive', - fillAlphaInactive / 100 - ); - - // we assume that if the user changes the inactive fill alpha, they - // want the inactive outline to be also changed - this._setLabelmapConfigValue( - 'outlineOpacityInactive', - Math.max(0.75, fillAlphaInactive / 100) // don't go below 0.7 for outline - ); - } - // if (brushSize !== undefined) { // const { toolGroupService } = this.servicesManager.services; @@ -1320,6 +1546,7 @@ class SegmentationService extends PubSubService { }); } } + public shouldRenderSegmentation( viewportDisplaySetInstanceUIDs, segDisplaySetInstanceUID @@ -1339,11 +1566,13 @@ class SegmentationService extends PubSubService { segDisplaySetInstanceUID ); - const segFrameOfReferenceUID = segDisplaySet.instance?.FrameOfReferenceUID; + const segFrameOfReferenceUID = this._getFrameOfReferenceUIDForSeg( + segDisplaySet + ); - viewportDisplaySetInstanceUIDs.forEach(displaySetInstanceUID => { - // check if the displaySet is sharing the same frameOfReferenceUID - // with the new segmentation + // check if the displaySet is sharing the same frameOfReferenceUID + // with the new segmentation + for (const displaySetInstanceUID of viewportDisplaySetInstanceUIDs) { const displaySet = displaySetService.getDisplaySetByUID( displaySetInstanceUID ); @@ -1355,12 +1584,29 @@ class SegmentationService extends PubSubService { displaySet?.images?.[0]?.FrameOfReferenceUID === segFrameOfReferenceUID ) { shouldDisplaySeg = true; + break; } - }); + } return shouldDisplaySeg; } + private _getDefaultSegmentationScheme() { + return { + activeSegmentIndex: 1, + cachedStats: {}, + label: '', + segmentsLocked: [], + displayText: [], + hydrated: false, // by default we don't hydrate the segmentation for SEG displaySets + segmentCount: 0, + segments: [], + isVisible: true, + isActive: false, + colorLUTIndex: 0, + }; + } + private _setActiveSegmentationForToolGroup( segmentationId: string, toolGroupId: string, @@ -1454,10 +1700,17 @@ class SegmentationService extends PubSubService { } } + private _getVolumeIdForDisplaySet(displaySet) { + const volumeLoaderSchema = + displaySet.volumeLoaderSchema ?? VOLUME_LOADER_SCHEME; + + return `${volumeLoaderSchema}:${displaySet.displaySetInstanceUID}`; + } + private _setSegmentColor = ( segmentationId: string, segmentIndex: number, - color: Types.Point3, + color: ohifTypes.RGB, toolGroupId?: string, suppressEvents = false ) => { @@ -1723,12 +1976,16 @@ class SegmentationService extends PubSubService { return representation; } - private _setLabelmapConfigValue = (property, value) => { + private _setSegmentationConfig = (property, value) => { + // Todo: currently we only support global config, and we get the type + // from the first segmentation + const typeToUse = this.getSegmentations()[0].type; + const { cornerstoneViewportService } = this.servicesManager.services; const config = cstSegmentation.config.getGlobalConfig(); - config.representations.LABELMAP[property] = value; + config.representations[typeToUse][property] = value; // Todo: add non global (representation specific config as well) cstSegmentation.config.setGlobalConfig(config); @@ -1743,7 +2000,7 @@ class SegmentationService extends PubSubService { // Connect Segmentation Service to Cornerstone3D. eventTarget.addEventListener( csToolsEnums.Events.SEGMENTATION_MODIFIED, - this._onSegmentationModified + this._onSegmentationModifiedFromSource ); eventTarget.addEventListener( @@ -1767,7 +2024,7 @@ class SegmentationService extends PubSubService { }); }; - private _onSegmentationModified = evt => { + private _onSegmentationModifiedFromSource = evt => { const { segmentationId } = evt.detail; const segmentation = this.segmentations[segmentationId]; @@ -1785,23 +2042,25 @@ class SegmentationService extends PubSubService { return; } - if (!Object.keys(segmentationState.representationData).includes(LABELMAP)) { - throw new Error('Non-labelmap representations are not supported yet'); - } - const { activeSegmentIndex, cachedStats, segmentsLocked, - representationData, label, type, } = segmentationState; - const labelmapRepresentationData = representationData[LABELMAP]; + if (![LABELMAP, CONTOUR].includes(type)) { + throw new Error( + `Unsupported segmentation type: ${type}. Only ${LABELMAP} and ${CONTOUR} are supported.` + ); + } + + const representationData = segmentationState.representationData[type]; // TODO: handle other representations when available in cornerstone3D const segmentationSchema = { + ...segmentation, activeSegmentIndex, cachedStats, displayText: [], @@ -1809,7 +2068,11 @@ class SegmentationService extends PubSubService { label, segmentsLocked, type, - volumeId: labelmapRepresentationData.volumeId, + representationData: { + [type]: { + ...representationData, + }, + }, }; try { @@ -1881,7 +2144,7 @@ class SegmentationService extends PubSubService { // cleanup the segmentation state too segmentationState.removeSegmentation(segmentationId); - if (removeFromCache) { + if (removeFromCache && cache.getVolumeLoadObject(segmentationId)) { cache.removeVolumeLoadObject(segmentationId); } } @@ -1965,6 +2228,22 @@ class SegmentationService extends PubSubService { return toolGroupIds; } + private _getFrameOfReferenceUIDForSeg(displaySet) { + const frameOfReferenceUID = displaySet.instance?.FrameOfReferenceUID; + + if (frameOfReferenceUID) { + return frameOfReferenceUID; + } + + // if not found we should try the ReferencedFrameOfReferenceSequence + const referencedFrameOfReferenceSequence = + displaySet.instance?.ReferencedFrameOfReferenceSequence; + + if (referencedFrameOfReferenceSequence) { + return referencedFrameOfReferenceSequence.FrameOfReferenceUID; + } + } + private _getFirstToolGroupId = () => { const { toolGroupService } = this.servicesManager.services; const toolGroupIds = toolGroupService.getToolGroupIds(); diff --git a/extensions/cornerstone/src/services/SegmentationService/SegmentationServiceTypes.ts b/extensions/cornerstone/src/services/SegmentationService/SegmentationServiceTypes.ts index 3d4066d09..e170197c3 100644 --- a/extensions/cornerstone/src/services/SegmentationService/SegmentationServiceTypes.ts +++ b/extensions/cornerstone/src/services/SegmentationService/SegmentationServiceTypes.ts @@ -29,6 +29,8 @@ type Segmentation = { colorLUTIndex: number; // if segmentation contains any data (often calculated from labelmap) cachedStats: Record; + // displaySetInstanceUID + displaySetInstanceUID: string; // displayText is the text that is displayed on the segmentation panel (often derived from the data) displayText?: string[]; // the id of the segmentation @@ -45,44 +47,22 @@ type Segmentation = { segments: Array; // the set of segments that are locked segmentsLocked: Array; - // the segmentation representation type - type: csToolsEnums.SegmentationRepresentations; - // if labelmap, the id of the volume that the labelmap is associated with - volumeId?: string; // whether the segmentation is hydrated or not (non-hydrated SEG -> temporary segmentation for display in SEG Viewport // but hydrated SEG -> segmentation that is persisted in the store) hydrated: boolean; -}; - -// Schema to generate a segmentation -type SegmentationSchema = { - // active segment index for the segmentation - activeSegmentIndex: number; - // statistics that are derived from the segmentation - cachedStats: Record; - // the displayText for the segmentation in the panels - displayText?: string[]; - // segmentation id - id: string; - // displaySetInstanceUID - displaySetInstanceUID: string; - // segmentation label - label: string; - // segment indices that are locked for the segmentation - segmentsLocked: Array; // the type of the segmentation (e.g., Labelmap etc.) type: csToolsEnums.SegmentationRepresentations; - // the volume id of the volume that the labelmap is associated with, this only exists for the labelmap representation - volumeId: string; - // the referenced volumeURI for the segmentation - referencedVolumeURI: string; - // whether the segmentation is hydrated or not (non-hydrated SEG -> temporary segmentation for display in SEG Viewport - // but hydrated SEG -> segmentation that is persisted in the store) - hydrated: boolean; - // the number of segments in the segmentation - segmentCount: number; - // the array of segments with their details - segments: Array; + // the segmentation representation data + representationData: SegmentationRepresentationData; }; -export { SegmentationConfig, Segment, Segmentation, SegmentationSchema }; +type LabelmapSegmentationData = { + volumeId: string; + referencedVolumeId?: string; +}; + +type SegmentationRepresentationData = { + LABELMAP?: LabelmapSegmentationData; +}; + +export { SegmentationConfig, Segment, Segmentation }; diff --git a/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts b/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts index a99083d8b..cf47cce78 100644 --- a/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts +++ b/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts @@ -11,9 +11,13 @@ import { cache, utilities, CONSTANTS, + Enums as csEnums, } from '@cornerstonejs/core'; -import { utilities as csToolsUtils } from '@cornerstonejs/tools'; +import { + utilities as csToolsUtils, + Enums as csToolsEnums, +} from '@cornerstonejs/tools'; import { IViewportService } from './IViewportService'; import { RENDERING_ENGINE_ID } from './constants'; import ViewportInfo, { @@ -386,7 +390,7 @@ class CornerstoneViewportService extends PubSubService initialImageIndexToUse === null ) { initialImageIndexToUse = - this._getInitialImageIndexForStackViewport(viewportInfo, imageIds) || 0; + this._getInitialImageIndexForViewport(viewportInfo, imageIds) || 0; } const properties = { ...presentations.lutPresentation?.properties }; @@ -412,7 +416,7 @@ class CornerstoneViewportService extends PubSubService }); } - private _getInitialImageIndexForStackViewport( + private _getInitialImageIndexForViewport( viewportInfo: ViewportInfo, imageIds?: string[] ): number { @@ -423,7 +427,29 @@ class CornerstoneViewportService extends PubSubService } const { index, preset } = initialImageOptions; - return this._getInitialImageIndex(imageIds.length, index, preset); + const viewportType = viewportInfo.getViewportType(); + + let numberOfSlices; + if (viewportType === csEnums.ViewportType.STACK) { + numberOfSlices = imageIds.length; + } else if (viewportType === csEnums.ViewportType.ORTHOGRAPHIC) { + const viewport = this.getCornerstoneViewport( + viewportInfo.getViewportId() + ); + const imageSliceData = csUtils.getImageSliceDataForVolumeViewport( + viewport + ); + + if (!imageSliceData) { + return; + } + + ({ numberOfSlices } = imageSliceData); + } else { + return; + } + + return this._getInitialImageIndex(numberOfSlices, index, preset); } _getInitialImageIndex( @@ -548,7 +574,6 @@ class CornerstoneViewportService extends PubSubService ) { const { displaySetService, - segmentationService, toolGroupService, } = this.servicesManager.services; @@ -558,110 +583,32 @@ class CornerstoneViewportService extends PubSubService // load any secondary displaySets const displaySetInstanceUIDs = this.viewportsDisplaySets.get(viewport.id); - const segDisplaySet = displaySetInstanceUIDs + // can be SEG or RTSTRUCT for now + const overlayDisplaySet = displaySetInstanceUIDs .map(displaySetService.getDisplaySetByUID) - .find(displaySet => displaySet && displaySet.Modality === 'SEG'); + .find(displaySet => displaySet?.isOverlayDisplaySet); - if (segDisplaySet) { - const { referencedVolumeId } = segDisplaySet; - const referencedVolume = cache.getVolume(referencedVolumeId); - const segmentationId = segDisplaySet.displaySetInstanceUID; - - const toolGroup = toolGroupService.getToolGroupForViewport(viewport.id); - - if (referencedVolume) { - segmentationService.addSegmentationRepresentationToToolGroup( - toolGroup.id, - segmentationId - ); - } + if (overlayDisplaySet) { + this.addOverlayRepresentationForDisplaySet(overlayDisplaySet, viewport); } else { - const toolGroup = toolGroupService.getToolGroupForViewport(viewport.id); - const toolGroupSegmentationRepresentations = - segmentationService.getSegmentationRepresentationsForToolGroup( - toolGroup.id - ) || []; - - // csToolsUtils.segmentation.triggerSegmentationRender(toolGroup.id); // If the displaySet is not a SEG displaySet we assume it is a primary displaySet // and we can look into hydrated segmentations to check if any of them are // associated with the primary displaySet + // get segmentations only returns the hydrated segmentations - const segmentations = segmentationService.getSegmentations(); - - for (const segmentation of segmentations) { - // if there is already a segmentation representation for this segmentation - // for this toolGroup, don't bother at all - if ( - toolGroupSegmentationRepresentations.find( - representation => representation.segmentationId === segmentation.id - ) - ) { - continue; - } - - // otherwise, check if the hydrated segmentations are in the same FOR - // as the primary displaySet, if so add the representation (since it was not there) - const { id: segDisplaySetInstanceUID } = segmentation; - - const segFrameOfReferenceUID = this._getFrameOfReferenceUID( - segDisplaySetInstanceUID - ); - - let shouldDisplaySeg = false; - - for (const displaySetInstanceUID of displaySetInstanceUIDs) { - const primaryFrameOfReferenceUID = this._getFrameOfReferenceUID( - displaySetInstanceUID - ); - - if (segFrameOfReferenceUID === primaryFrameOfReferenceUID) { - shouldDisplaySeg = true; - break; - } - } - - if (shouldDisplaySeg) { - const toolGroup = toolGroupService.getToolGroupForViewport( - viewport.id - ); - - segmentationService.addSegmentationRepresentationToToolGroup( - toolGroup.id, - segmentation.id - ); - } - } + this._addSegmentationRepresentationToToolGroupIfNecessary( + displaySetInstanceUIDs, + viewport + ); } const viewportInfo = this.getViewportInfo(viewport.id); - - if (!viewportInfo) { - console.warn('Viewport info not defined for', viewport.id); - } - const toolGroup = toolGroupService.getToolGroupForViewport(viewport.id); csToolsUtils.segmentation.triggerSegmentationRender(toolGroup.id); - const initialImageOptions = viewportInfo.getInitialImageOptions(); - - if ( - initialImageOptions && - (initialImageOptions.preset !== undefined || - initialImageOptions.index !== undefined) - ) { - const { index, preset } = initialImageOptions; - - const { numberOfSlices } = csUtils.getImageSliceDataForVolumeViewport( - viewport - ); - - const imageIndex = this._getInitialImageIndex( - numberOfSlices, - index, - preset - ); + const imageIndex = this._getInitialImageIndexForViewport(viewportInfo); + if (imageIndex !== undefined) { csToolsUtils.jumpToSlice(viewport.element, { imageIndex, }); @@ -670,6 +617,96 @@ class CornerstoneViewportService extends PubSubService viewport.render(); } + private _addSegmentationRepresentationToToolGroupIfNecessary( + displaySetInstanceUIDs: string[], + viewport: any + ) { + const { + segmentationService, + toolGroupService, + } = this.servicesManager.services; + + const toolGroup = toolGroupService.getToolGroupForViewport(viewport.id); + + // this only returns hydrated segmentations + const segmentations = segmentationService.getSegmentations(); + + for (const segmentation of segmentations) { + const toolGroupSegmentationRepresentations = + segmentationService.getSegmentationRepresentationsForToolGroup( + toolGroup.id + ) || []; + + // if there is already a segmentation representation for this segmentation + // for this toolGroup, don't bother at all + const isSegmentationInToolGroup = toolGroupSegmentationRepresentations.find( + representation => representation.segmentationId === segmentation.id + ); + + if (isSegmentationInToolGroup) { + continue; + } + + // otherwise, check if the hydrated segmentations are in the same FOR + // as the primary displaySet, if so add the representation (since it was not there) + const { id: segDisplaySetInstanceUID, type } = segmentation; + const segFrameOfReferenceUID = this._getFrameOfReferenceUID( + segDisplaySetInstanceUID + ); + + let shouldDisplaySeg = false; + + for (const displaySetInstanceUID of displaySetInstanceUIDs) { + const primaryFrameOfReferenceUID = this._getFrameOfReferenceUID( + displaySetInstanceUID + ); + + if (segFrameOfReferenceUID === primaryFrameOfReferenceUID) { + shouldDisplaySeg = true; + break; + } + } + + if (!shouldDisplaySeg) { + return; + } + + segmentationService.addSegmentationRepresentationToToolGroup( + toolGroup.id, + segmentation.id, + false, // already hydrated, + segmentation.type + ); + } + } + + private addOverlayRepresentationForDisplaySet( + displaySet: any, + viewport: any + ) { + const { + segmentationService, + toolGroupService, + } = this.servicesManager.services; + + const { referencedVolumeId } = displaySet; + const segmentationId = displaySet.displaySetInstanceUID; + + const toolGroup = toolGroupService.getToolGroupForViewport(viewport.id); + + const representationType = + referencedVolumeId && cache.getVolume(referencedVolumeId) !== undefined + ? csToolsEnums.SegmentationRepresentations.Labelmap + : csToolsEnums.SegmentationRepresentations.Contour; + + segmentationService.addSegmentationRepresentationToToolGroup( + toolGroup.id, + segmentationId, + false, + representationType + ); + } + // Todo: keepCamera is an interim solution until we have a better solution for // keeping the camera position when the viewport data is changed public updateViewport( @@ -859,6 +896,11 @@ class CornerstoneViewportService extends PubSubService return instance.FrameOfReferenceUID; } + if (displaySet.Modality === 'RTSTRUCT') { + const { instance } = displaySet; + return instance.ReferencedFrameOfReferenceSequence.FrameOfReferenceUID; + } + const { images } = displaySet; if (images && images.length) { return images[0].FrameOfReferenceUID; diff --git a/extensions/cornerstone/src/utils/transitions.ts b/extensions/cornerstone/src/utils/transitions.ts index 2fa96794d..28d2dacd0 100644 --- a/extensions/cornerstone/src/utils/transitions.ts +++ b/extensions/cornerstone/src/utils/transitions.ts @@ -20,3 +20,17 @@ export function easeInOutBell(x: number, baseline: number): number { return (- 4 * Math.pow(2 * x - 2, 3)) * alpha + baseline; } } + +/** + * A reversed bell curved function that starts from 1 and goes to baseline and + * come back to 1 again. It uses ease in out quadratic for css transition + * timing function for each side of the curve. + * + * @param {number} x - The current time, in the range [0, 1]. + * @param {number} baseline - The baseline value to start from and return to. + * @returns the value of the transition at time x. + */ +export function reverseEaseInOutBell(x: number, baseline: number): number { + const y = easeInOutBell(x, baseline); + return -y + 1 + baseline; +} diff --git a/extensions/default/src/DicomWebDataSource/index.js b/extensions/default/src/DicomWebDataSource/index.js index 3534c727d..792ee44c7 100644 --- a/extensions/default/src/DicomWebDataSource/index.js +++ b/extensions/default/src/DicomWebDataSource/index.js @@ -178,6 +178,17 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) { directURL: params => { return getDirectURL(wadoRoot, params); }, + bulkDataURI: async ({ StudyInstanceUID, BulkDataURI }) => { + const options = { + multipart: false, + BulkDataURI, + StudyInstanceUID, + }; + return qidoDicomWebClient.retrieveBulkData(options).then(val => { + const ret = (val && val[0]) || undefined; + return ret; + }); + }, series: { metadata: async ({ StudyInstanceUID, diff --git a/extensions/default/src/getSopClassHandlerModule.js b/extensions/default/src/getSopClassHandlerModule.js index f00018187..df1900051 100644 --- a/extensions/default/src/getSopClassHandlerModule.js +++ b/extensions/default/src/getSopClassHandlerModule.js @@ -14,7 +14,10 @@ const makeDisplaySet = instances => { const instance = instances[0]; const imageSet = new ImageSet(instances); - const displayReconstructableInfo = isDisplaySetReconstructable(instances); + const { + value: isReconstructable, + averageSpacingBetweenFrames, + } = isDisplaySetReconstructable(instances); // set appropriate attributes to image set... imageSet.setAttributes({ @@ -29,10 +32,11 @@ const makeDisplaySet = instances => { SeriesDescription: instance.SeriesDescription || '', Modality: instance.Modality, isMultiFrame: isMultiFrame(instance), - countIcon: displayReconstructableInfo.value ? 'icon-mpr' : undefined, + countIcon: isReconstructable ? 'icon-mpr' : undefined, numImageFrames: instances.length, SOPClassHandlerId: `${id}.sopClassHandlerModule.${sopClassHandlerName}`, - isReconstructable: displayReconstructableInfo.value, + isReconstructable, + averageSpacingBetweenFrames: averageSpacingBetweenFrames || null, }); // Sort the images in this series if needed diff --git a/extensions/measurement-tracking/package.json b/extensions/measurement-tracking/package.json index b07b17d2e..a695b0268 100644 --- a/extensions/measurement-tracking/package.json +++ b/extensions/measurement-tracking/package.json @@ -33,7 +33,7 @@ "@ohif/core": "^3.0.0", "classnames": "^2.3.2", "@cornerstonejs/core": "^0.42.2", - "@cornerstonejs/tools": "^0.61.11", + "@cornerstonejs/tools": "^0.63.2", "@ohif/extension-cornerstone-dicom-sr": "^3.0.0", "dcmjs": "^0.29.5", "lodash.debounce": "^4.17.21", diff --git a/modes/longitudinal/package.json b/modes/longitudinal/package.json index 7a35b2b9a..32cd0ed37 100644 --- a/modes/longitudinal/package.json +++ b/modes/longitudinal/package.json @@ -36,6 +36,8 @@ "@ohif/extension-default": "^3.0.0", "@ohif/extension-cornerstone": "^3.0.0", "@ohif/extension-cornerstone-dicom-sr": "^3.0.0", + "@ohif/extension-cornerstone-dicom-seg": "^3.0.0", + "@ohif/extension-cornerstone-dicom-rt": "^3.0.0", "@ohif/extension-dicom-pdf": "^3.0.1", "@ohif/extension-dicom-video": "^3.0.1", "@ohif/extension-measurement-tracking": "^3.0.0" diff --git a/modes/longitudinal/src/index.js b/modes/longitudinal/src/index.js index 6e2d8a2da..4f882c457 100644 --- a/modes/longitudinal/src/index.js +++ b/modes/longitudinal/src/index.js @@ -5,7 +5,7 @@ import initToolGroups from './initToolGroups.js'; // Allow this mode by excluding non-imaging modalities such as SR, SEG // Also, SM is not a simple imaging modalities, so exclude it. -const NON_IMAGE_MODALITIES = ['SM', 'ECG', 'SR', 'SEG']; +const NON_IMAGE_MODALITIES = ['SM', 'ECG', 'SR', 'SEG', 'RTSTRUCT']; const ohif = { layout: '@ohif/extension-default.layoutTemplateModule.viewerLayout', @@ -45,6 +45,12 @@ const dicomSeg = { panel: '@ohif/extension-cornerstone-dicom-seg.panelModule.panelSegmentation', }; +const dicomRt = { + viewport: '@ohif/extension-cornerstone-dicom-rt.viewportModule.dicom-rt', + sopClassHandler: + '@ohif/extension-cornerstone-dicom-rt.sopClassHandlerModule.dicom-rt', +}; + const extensionDependencies = { // Can derive the versions at least process.env.from npm_package_version '@ohif/extension-default': '^3.0.0', @@ -52,6 +58,7 @@ const extensionDependencies = { '@ohif/extension-measurement-tracking': '^3.0.0', '@ohif/extension-cornerstone-dicom-sr': '^3.0.0', '@ohif/extension-cornerstone-dicom-seg': '^3.0.0', + '@ohif/extension-cornerstone-dicom-rt': '^3.0.0', '@ohif/extension-dicom-pdf': '^3.0.1', '@ohif/extension-dicom-video': '^3.0.1', }; @@ -211,6 +218,10 @@ function modeFactory() { namespace: dicomSeg.viewport, displaySetsToDisplay: [dicomSeg.sopClassHandler], }, + { + namespace: dicomRt.viewport, + displaySetsToDisplay: [dicomRt.sopClassHandler], + }, ], }, }; @@ -230,6 +241,7 @@ function modeFactory() { ohif.sopClassHandler, dicompdf.sopClassHandler, dicomsr.sopClassHandler, + dicomRt.sopClassHandler, ], hotkeys: [...hotkeys.defaults.hotkeyBindings], }; diff --git a/platform/core/src/classes/ImageSet.js b/platform/core/src/classes/ImageSet.ts similarity index 72% rename from platform/core/src/classes/ImageSet.js rename to platform/core/src/classes/ImageSet.ts index 80838c14f..d7ac82bce 100644 --- a/platform/core/src/classes/ImageSet.js +++ b/platform/core/src/classes/ImageSet.ts @@ -1,7 +1,16 @@ import guid from '../utils/guid.js'; import { Vector3 } from 'cornerstone-math'; -const OBJECT = 'object'; +type Attributes = Record; +type Image = { + StudyInstanceUID?: string; + getData(): { + metadata: { + ImagePositionPatient: number[]; + ImageOrientationPatient: number[]; + }; + }; +}; /** * This class defines an ImageSet object which will be used across the viewer. This object represents @@ -10,8 +19,14 @@ const OBJECT = 'object'; * indiscriminately, but this should be changed). */ class ImageSet { - constructor(images) { - if (Array.isArray(images) !== true) { + images: Image[]; + uid: string; + instances: Image[]; + instance?: Image; + StudyInstanceUID?: string; + + constructor(images: Image[]) { + if (!Array.isArray(images)) { throw new Error('ImageSet expects an array of images'); } @@ -36,41 +51,39 @@ class ImageSet { this.StudyInstanceUID = this.instance?.StudyInstanceUID; } - getUID() { + load: () => Promise; + + getUID(): string { return this.uid; } - setAttribute(attribute, value) { + setAttribute(attribute: string, value: unknown): void { this[attribute] = value; } - getAttribute(attribute) { + getAttribute(attribute: string): unknown { return this[attribute]; } - setAttributes(attributes) { - if (typeof attributes === OBJECT && attributes !== null) { - const imageSet = this, - hasOwn = Object.prototype.hasOwnProperty; - for (let attribute in attributes) { - if (hasOwn.call(attributes, attribute)) { - imageSet[attribute] = attributes[attribute]; - } + setAttributes(attributes: Attributes): void { + if (typeof attributes === 'object' && attributes !== null) { + for (const [attribute, value] of Object.entries(attributes)) { + this[attribute] = value; } } } - getNumImages = () => this.images.length; + getNumImages = (): number => this.images.length; - getImage(index) { + getImage(index: number): Image { return this.images[index]; } - sortBy(sortingCallback) { + sortBy(sortingCallback: (a: Image, b: Image) => number): Image[] { return this.images.sort(sortingCallback); } - sortByImagePositionPatient() { + sortByImagePositionPatient(): void { const images = this.images; const referenceImagePositionPatient = _getImagePositionPatient(images[0]); @@ -94,7 +107,7 @@ class ImageSet { ) ); - const distanceImagePairs = images.map(function(image) { + const distanceImagePairs = images.map(function(image: Image) { const ippVec = new Vector3(..._getImagePositionPatient(image)); const positionVector = refIppVec.clone().sub(ippVec); const distance = positionVector.dot(scanAxisNormal); diff --git a/platform/core/src/extensions/ExtensionManager.ts b/platform/core/src/extensions/ExtensionManager.ts index 9c26d7370..c028fbab3 100644 --- a/platform/core/src/extensions/ExtensionManager.ts +++ b/platform/core/src/extensions/ExtensionManager.ts @@ -41,6 +41,7 @@ export interface Extension { getCommandsModule?: (p: ExtensionParams) => CommandsModule; getViewportModule?: (p: ExtensionParams) => unknown; getUtilityModule?: (p: ExtensionParams) => unknown; + getCustomizationModule?: (p: ExtensionParams) => unknown; onModeEnter?: () => void; onModeExit?: () => void; } diff --git a/platform/core/src/types/Color.ts b/platform/core/src/types/Color.ts new file mode 100644 index 000000000..7dfacefb6 --- /dev/null +++ b/platform/core/src/types/Color.ts @@ -0,0 +1,4 @@ +/** + * RGB color type + */ +export type RGB = [number, number, number]; diff --git a/platform/core/src/types/index.ts b/platform/core/src/types/index.ts index 089a994f5..3c68b60c4 100644 --- a/platform/core/src/types/index.ts +++ b/platform/core/src/types/index.ts @@ -12,6 +12,7 @@ export * from './Command'; export * from './StudyMetadata'; export * from './PanelModule'; export * from './IPubSub'; +export * from './Color'; /** * Export the types used within the various services and managers, but diff --git a/platform/docs/docs/platform/services/data/SegmentationService.md b/platform/docs/docs/platform/services/data/SegmentationService.md index fcde850bc..54e7f82a7 100644 --- a/platform/docs/docs/platform/services/data/SegmentationService.md +++ b/platform/docs/docs/platform/services/data/SegmentationService.md @@ -25,8 +25,8 @@ There are seven events that get publish in `MeasurementService`: | SEGMENTATION_ADDED | Fires when a new segmentation is added to OHIF | | SEGMENTATION_REMOVED | Fires when a segmentation is removed from OHIF | | SEGMENTATION_CONFIGURATION_CHANGED | Fires when a segmentation configuration is changed | -| SEGMENT_PIXEL_DATA_CREATED | Fires when a segment group adds its pixel data to the volume | -| SEGMENTATION_PIXEL_DATA_CREATED | Fires when the full segmentation volume is filled with its segments | +| SEGMENT_LOADING_COMPLETE | Fires when a segment group adds its pixel data to the volume | +| SEGMENTATION_LOADING_COMPLETE | Fires when the full segmentation volume is filled with its segments | ## API diff --git a/platform/ui/src/components/InputNumber/InputNumber.tsx b/platform/ui/src/components/InputNumber/InputNumber.tsx index 185420eab..a96446293 100644 --- a/platform/ui/src/components/InputNumber/InputNumber.tsx +++ b/platform/ui/src/components/InputNumber/InputNumber.tsx @@ -19,37 +19,60 @@ const sizesClasses = { const InputNumber: React.FC<{ value: number; onChange: (value) => void; + minValue?: number; + maxValue?: number; step: number; size?: string; className?: string; -}> = ({ value, onChange, step = 1, className, size = 'sm' }) => { +}> = ({ + value, + onChange, + step = 1, + className, + size = 'sm', + minValue = 0, + maxValue = 100, +}) => { const [numberValue, setNumberValue] = useState(value); + const handleMinMax = useCallback( + (value: number) => { + if (value > maxValue) { + return maxValue; + } else if (value < minValue) { + return minValue; + } else { + return value; + } + }, + [maxValue, minValue] + ); + const handleChange = useCallback( e => { - const numberValue = e.target.value; + const numberValue = handleMinMax(Number(e.target.value)); setNumberValue(numberValue); onChange(numberValue); }, - [onChange, setNumberValue] + [onChange, setNumberValue, handleMinMax] ); const handleIncrement = useCallback( e => { - const newNum = Number(numberValue) + step; + const newNum = handleMinMax(Number(numberValue) + step); setNumberValue(newNum); onChange(newNum); }, - [onChange, setNumberValue, step, numberValue] + [onChange, setNumberValue, step, numberValue, handleMinMax] ); const handleDecrement = useCallback( e => { - const newNum = Number(numberValue) - step; + const newNum = handleMinMax(Number(numberValue) - step); setNumberValue(newNum); onChange(newNum); }, - [onChange, setNumberValue, step, numberValue] + [onChange, setNumberValue, step, numberValue, handleMinMax] ); return ( diff --git a/platform/ui/src/components/InputRange/InputRange.tsx b/platform/ui/src/components/InputRange/InputRange.tsx index 28e98b06f..9bcf40b14 100644 --- a/platform/ui/src/components/InputRange/InputRange.tsx +++ b/platform/ui/src/components/InputRange/InputRange.tsx @@ -54,6 +54,9 @@ const InputRange: React.FC<{ const rangeValuePercentage = ((rangeValue - minValue) / (maxValue - minValue)) * 100; + const rangeValueForStr = + step >= 1 ? rangeValue.toFixed(0) : rangeValue.toFixed(1); + return (
- {rangeValue} + {rangeValueForStr} {unit} )} diff --git a/platform/ui/src/components/LoadingIndicatorTotalPercent/LoadingIndicatorTotalPercent.tsx b/platform/ui/src/components/LoadingIndicatorTotalPercent/LoadingIndicatorTotalPercent.tsx new file mode 100644 index 000000000..4a649e453 --- /dev/null +++ b/platform/ui/src/components/LoadingIndicatorTotalPercent/LoadingIndicatorTotalPercent.tsx @@ -0,0 +1,54 @@ +import React from 'react'; + +import LoadingIndicatorProgress from '../LoadingIndicatorProgress'; + +interface Props { + className?: string; + totalNumbers: number | null; + percentComplete: number | null; + loadingText?: string; + targetText?: string; +} + +/** + * A React component that renders a loading indicator but accepts a totalNumbers + * and percentComplete to display a more detailed message. + */ +function LoadingIndicatorTotalPercent({ + className, + totalNumbers, + percentComplete, + loadingText = 'Loading...', + targetText = 'segments', +}: Props): JSX.Element { + percentComplete = percentComplete !== null ? percentComplete : null; + + const progress = percentComplete !== null ? percentComplete : null; + const totalNumbersText = totalNumbers !== null ? `${totalNumbers}` : ''; + const numTargetsLoadedText = + percentComplete !== null + ? Math.floor((percentComplete * totalNumbers) / 100) + : ''; + + const textBlock = !totalNumbers ? ( +
{loadingText}
+ ) : ( +
+
Loaded
+
{numTargetsLoadedText}
+
of
+
{totalNumbersText}
+
{targetText}
+
+ ); + + return ( + + ); +} + +export default LoadingIndicatorTotalPercent; diff --git a/platform/ui/src/components/LoadingIndicatorTotalPercent/index.js b/platform/ui/src/components/LoadingIndicatorTotalPercent/index.js new file mode 100644 index 000000000..fc4e1fa10 --- /dev/null +++ b/platform/ui/src/components/LoadingIndicatorTotalPercent/index.js @@ -0,0 +1,2 @@ +import LoadingIndicatorTotalPercent from './LoadingIndicatorTotalPercent'; +export default LoadingIndicatorTotalPercent; diff --git a/platform/ui/src/components/SegmentationGroupTable/SegmentationConfig.tsx b/platform/ui/src/components/SegmentationGroupTable/SegmentationConfig.tsx index 6167ec55d..8a83e567e 100644 --- a/platform/ui/src/components/SegmentationGroupTable/SegmentationConfig.tsx +++ b/platform/ui/src/components/SegmentationGroupTable/SegmentationConfig.tsx @@ -1,27 +1,15 @@ import React, { useState } from 'react'; import { Icon, InputRange, CheckBox, InputNumber } from '../'; import classNames from 'classnames'; -import { reducer } from './segmentationConfigReducer'; const ActiveSegmentationConfig = ({ config, - dispatch, setRenderOutline, setOutlineOpacityActive, setOutlineWidthActive, setRenderFill, setFillAlpha, - usePercentage, }) => { - const [ - useOutlineOpacityPercentage, - setUseOutlineOpacityPercentage, - ] = useState(usePercentage); - - const [useFillAlphaPercentage, setUseFillAlphaPercentage] = useState( - usePercentage - ); - return (
@@ -31,32 +19,14 @@ const ActiveSegmentationConfig = ({ checked={config.renderOutline} labelClassName="text-[12px] pl-1 pt-1" className="mb-[9px]" - onChange={value => { - dispatch({ - type: 'RENDER_OUTLINE', - payload: { - value, - }, - }); - - setRenderOutline(value); - }} + onChange={setRenderOutline} /> { - dispatch({ - type: 'RENDER_FILL', - payload: { - value, - }, - }); - - setRenderFill(value); - }} + onChange={setRenderFill} />
@@ -64,23 +34,9 @@ const ActiveSegmentationConfig = ({
Opacity
{ - setUseOutlineOpacityPercentage(false); - dispatch({ - type: 'SET_OUTLINE_OPACITY', - payload: { - value: value, - }, - }); - - setOutlineOpacityActive(value); - }} + maxValue={100} + value={config.outlineOpacity * 100} + onChange={setOutlineOpacityActive} step={1} containerClassName="mt-[4px] mb-[9px]" inputClassName="w-[64px]" @@ -89,21 +45,9 @@ const ActiveSegmentationConfig = ({ /> { - setUseFillAlphaPercentage(false); - dispatch({ - type: 'SET_FILL_ALPHA', - payload: { - value, - }, - }); - - setFillAlpha(value); - }} + maxValue={100} + value={config.fillAlpha * 100} + onChange={setFillAlpha} step={1} containerClassName="mt-[4px] mb-[9px]" inputClassName="w-[64px]" @@ -116,16 +60,9 @@ const ActiveSegmentationConfig = ({
Size
{ - dispatch({ - type: 'SET_OUTLINE_WIDTH', - payload: { - value, - }, - }); - - setOutlineWidthActive(value); - }} + onChange={setOutlineWidthActive} + minValue={0} + maxValue={10} className="-mt-1" />
@@ -135,16 +72,9 @@ const ActiveSegmentationConfig = ({ const InactiveSegmentationConfig = ({ config, - dispatch, setRenderInactiveSegmentations, setFillAlphaInactive, - usePercentage, }) => { - const [ - useFillAlphaInactivePercentage, - setUseFillInactivePercentage, - ] = useState(usePercentage); - return (
{ - dispatch({ - type: 'RENDER_INACTIVE_SEGMENTATIONS', - payload: { - value, - }, - }); - - setRenderInactiveSegmentations(value); - }} + onChange={setRenderInactiveSegmentations} />
Opacity { - setUseFillInactivePercentage(false); - dispatch({ - type: 'SET_FILL_ALPHA_INACTIVE', - payload: { - value: value, - }, - }); - - setFillAlphaInactive(value); - }} + maxValue={100} + value={config.fillAlphaInactive * 100} + onChange={setFillAlphaInactive} step={1} containerClassName="mt-[4px]" inputClassName="w-[64px]" @@ -206,11 +113,7 @@ const SegmentationConfig = ({ setRenderInactiveSegmentations, setRenderOutline, }) => { - const [config, dispatch] = React.useReducer( - reducer, - segmentationConfig.initialConfig - ); - + const { initialConfig } = segmentationConfig; const [isMinimized, setIsMinimized] = useState(true); return (
@@ -238,14 +141,12 @@ const SegmentationConfig = ({ {!isMinimized && (
{/* A small line */}
@@ -259,11 +160,9 @@ const SegmentationConfig = ({
)} diff --git a/platform/ui/src/components/SegmentationGroupTable/SegmentationGroupTable.tsx b/platform/ui/src/components/SegmentationGroupTable/SegmentationGroupTable.tsx index d6269cde2..42bb3f2d8 100644 --- a/platform/ui/src/components/SegmentationGroupTable/SegmentationGroupTable.tsx +++ b/platform/ui/src/components/SegmentationGroupTable/SegmentationGroupTable.tsx @@ -4,30 +4,6 @@ import Icon from '../Icon'; import SegmentationGroup from './SegmentationGroup'; import SegmentationConfig from './SegmentationConfig'; -const GetSegmentationConfig = ({ - setFillAlpha, - setFillAlphaInactive, - setOutlineWidthActive, - setRenderFill, - setRenderInactiveSegmentations, - setRenderOutline, - setOutlineOpacityActive, - segmentationConfig, -}) => { - return ( - - ); -}; - const SegmentationGroupTable = ({ segmentations, onSegmentationAdd, @@ -56,10 +32,7 @@ const SegmentationGroupTable = ({ }) => { return (
-
{!!segmentations.length && @@ -155,7 +129,6 @@ SegmentationGroupTable.defaultProps = { renderInactiveSegmentations: true, renderOutline: true, }, - usePercentage: true, }, setFillAlpha: () => {}, setFillAlphaInactive: () => {}, diff --git a/platform/ui/src/components/SegmentationGroupTable/segmentationConfigReducer.tsx b/platform/ui/src/components/SegmentationGroupTable/segmentationConfigReducer.tsx deleted file mode 100644 index 1063b0558..000000000 --- a/platform/ui/src/components/SegmentationGroupTable/segmentationConfigReducer.tsx +++ /dev/null @@ -1,22 +0,0 @@ -const reducer = (state, action) => { - switch (action.type) { - case 'RENDER_OUTLINE': - return { ...state, renderOutline: action.payload.value }; - case 'RENDER_FILL': - return { ...state, renderFill: action.payload.value }; - case 'SET_OUTLINE_OPACITY': - return { ...state, outlineOpacity: action.payload.value }; - case 'SET_OUTLINE_WIDTH': - return { ...state, outlineWidth: action.payload.value }; - case 'SET_FILL_ALPHA': - return { ...state, fillAlpha: action.payload.value }; - case 'SET_FILL_ALPHA_INACTIVE': - return { ...state, fillAlphaInactive: action.payload.value }; - case 'RENDER_INACTIVE_SEGMENTATIONS': - return { ...state, renderInactiveSegmentations: action.payload.value }; - default: - return state; - } -}; - -export { reducer }; diff --git a/platform/ui/src/components/index.js b/platform/ui/src/components/index.js index 4f70ef69c..d01247542 100644 --- a/platform/ui/src/components/index.js +++ b/platform/ui/src/components/index.js @@ -68,6 +68,7 @@ import InputRange from './InputRange'; import InputNumber from './InputNumber'; import CheckBox from './CheckBox'; import LoadingIndicatorProgress from './LoadingIndicatorProgress'; +import LoadingIndicatorTotalPercent from './LoadingIndicatorTotalPercent'; import ViewportActionBar from './ViewportActionBar'; export { @@ -104,6 +105,7 @@ export { LegacyCinePlayer, LegacyViewportActionBar, LoadingIndicatorProgress, + LoadingIndicatorTotalPercent, MeasurementTable, Modal, NavBar, diff --git a/platform/ui/src/index.js b/platform/ui/src/index.js index 50842160d..fad709a2c 100644 --- a/platform/ui/src/index.js +++ b/platform/ui/src/index.js @@ -65,6 +65,7 @@ export { LegacyCinePlayer, LegacyViewportActionBar, LoadingIndicatorProgress, + LoadingIndicatorTotalPercent, MeasurementTable, Modal, NavBar, diff --git a/platform/viewer/netlify.toml b/platform/viewer/netlify.toml index 468eca951..4af3dd597 100644 --- a/platform/viewer/netlify.toml +++ b/platform/viewer/netlify.toml @@ -12,7 +12,6 @@ base = "" build = "yarn run build:viewer:ci" publish = "dist" - ignore = "git diff --quiet $CACHED_COMMIT_REF $COMMIT_REF . ../ui/ ../core/ ../i18n" # NODE_VERSION in root `.nvmrc` takes priority diff --git a/platform/viewer/package.json b/platform/viewer/package.json index 2c1c7325b..fca0b294c 100644 --- a/platform/viewer/package.json +++ b/platform/viewer/package.json @@ -51,6 +51,7 @@ "@ohif/extension-cornerstone": "^3.0.0", "@ohif/extension-cornerstone-dicom-seg": "^3.0.0", "@ohif/extension-cornerstone-dicom-sr": "^3.0.0", + "@ohif/extension-cornerstone-dicom-rt": "^3.0.0", "@ohif/extension-default": "^3.0.0", "@ohif/extension-dicom-pdf": "^3.0.1", "@ohif/extension-dicom-video": "^3.0.1", diff --git a/platform/viewer/pluginConfig.json b/platform/viewer/pluginConfig.json index f69de2770..8c5d24197 100644 --- a/platform/viewer/pluginConfig.json +++ b/platform/viewer/pluginConfig.json @@ -31,6 +31,10 @@ { "packageName": "@ohif/extension-cornerstone-dicom-seg", "version": "3.0.0" + }, + { + "packageName": "@ohif/extension-cornerstone-dicom-rt", + "version": "3.0.0" } ], "modes": [ @@ -45,4 +49,4 @@ ], "modesFactory": [], "umd": [] -} \ No newline at end of file +} diff --git a/platform/viewer/public/config/default.js b/platform/viewer/public/config/default.js index 7b432830b..558f473c2 100644 --- a/platform/viewer/public/config/default.js +++ b/platform/viewer/public/config/default.js @@ -50,6 +50,7 @@ window.config = { supportsWildcard: true, staticWado: true, singlepart: 'bulkdata,video,pdf', + useBulkDataURI: false, }, }, { diff --git a/platform/viewer/public/config/demo.js b/platform/viewer/public/config/demo.js index 5c37f5b48..433d56845 100644 --- a/platform/viewer/public/config/demo.js +++ b/platform/viewer/public/config/demo.js @@ -18,6 +18,7 @@ window.config = { imageRendering: 'wadors', thumbnailRendering: 'wadors', enableStudyLazyLoad: true, + useBulkDataURI: false, }, ], }, diff --git a/platform/viewer/public/config/local_dcm4chee.js b/platform/viewer/public/config/local_dcm4chee.js index fca1f2a71..28ae28fd9 100644 --- a/platform/viewer/public/config/local_dcm4chee.js +++ b/platform/viewer/public/config/local_dcm4chee.js @@ -16,13 +16,14 @@ window.config = { sourceName: 'dicomweb', configuration: { name: 'DCM4CHEE', - wadoUriRoot: 'http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/wado', - qidoRoot: 'http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs', - wadoRoot: 'http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs', + wadoUriRoot: 'http://localhost/dcm4chee-arc/aets/DCM4CHEE/wado', + qidoRoot: 'http://localhost/dcm4chee-arc/aets/DCM4CHEE/rs', + wadoRoot: 'http://localhost/dcm4chee-arc/aets/DCM4CHEE/rs', qidoSupportsIncludeField: true, imageRendering: 'wadors', enableStudyLazyLoad: true, thumbnailRendering: 'wadors', + useBulkDataURI: false, requestOptions: { auth: 'admin:admin', }, diff --git a/platform/viewer/public/config/local_orthanc.js b/platform/viewer/public/config/local_orthanc.js index 5165cb7e5..71bacacbe 100644 --- a/platform/viewer/public/config/local_orthanc.js +++ b/platform/viewer/public/config/local_orthanc.js @@ -25,6 +25,7 @@ window.config = { imageRendering: 'wadors', thumbnailRendering: 'wadors', enableStudyLazyLoad: true, + useBulkDataURI: false, supportsFuzzyMatching: true, supportsWildcard: true, }, diff --git a/yarn.lock b/yarn.lock index 113a1eb55..032805b51 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1308,7 +1308,7 @@ core-js-pure "^3.25.1" regenerator-runtime "^0.13.11" -"@babel/runtime@7.17.9", "@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.10.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.14.6", "@babel/runtime@^7.17.8", "@babel/runtime@^7.18.6", "@babel/runtime@^7.20.13", "@babel/runtime@^7.20.7", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.0", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.2", "@babel/runtime@^7.7.4", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.9.2": +"@babel/runtime@7.17.9", "@babel/runtime@7.7.6", "@babel/runtime@^7.0.0", "@babel/runtime@^7.1.2", "@babel/runtime@^7.10.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.14.6", "@babel/runtime@^7.17.8", "@babel/runtime@^7.18.6", "@babel/runtime@^7.20.13", "@babel/runtime@^7.20.7", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.0", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.2", "@babel/runtime@^7.7.4", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.9.2": version "7.20.13" resolved "https://registry.npmjs.org/@babel/runtime/-/runtime-7.20.13.tgz#7055ab8a7cff2b8f6058bf6ae45ff84ad2aded4b" integrity sha512-gt3PKXs0DBoL9xCvOIIZ2NEqAGZqHjAnmVbfQtB620V0uReIQutpel14KcneZuer7UioY8ALKZ7iocavvzTNFA== @@ -1443,10 +1443,10 @@ resolved "https://registry.npmjs.org/@cornerstonejs/codec-openjph/-/codec-openjph-2.4.2.tgz#e96721d56f6ec96f7f95c16321d88cc8467d8d81" integrity sha512-lgdvBvvNezleY+4pIe2ceUsJzlZe/0PipdeubQ3vZZOz3xxtHHMR1XFCl4fgd8gosR8COHuD7h6q+MwgrwBsng== -"@cornerstonejs/core@^0.40.0": - version "0.40.0" - resolved "https://registry.npmjs.org/@cornerstonejs/core/-/core-0.40.0.tgz#5b6409277362b26c6ddb55b54025ecf26b304f84" - integrity sha512-tjUGFyXuRNRSybpKpd/mP4tKMshc48n/TIt9x5mXU+zqywBPGmojkXOj/v+pG02XopKLg5XPSI4LPysZNVscsg== +"@cornerstonejs/core@^0.41.0": + version "0.41.0" + resolved "https://registry.npmjs.org/@cornerstonejs/core/-/core-0.41.0.tgz#1268bc9cb70e101b52e5eee9055a84541d76ef5d" + integrity sha512-Wk4BpDaKYz9KRr6eNiYatxg/ZNsluNN2p5QsK0qNYyquR5ABo/fuBexI160plP3jI4pDKlMH+OpbXuLx3T3ngw== dependencies: detect-gpu "^4.0.45" lodash.clonedeep "4.5.0" @@ -1459,20 +1459,28 @@ detect-gpu "^4.0.45" lodash.clonedeep "4.5.0" -"@cornerstonejs/streaming-image-volume-loader@^0.16.0": - version "0.16.0" - resolved "https://registry.npmjs.org/@cornerstonejs/streaming-image-volume-loader/-/streaming-image-volume-loader-0.16.0.tgz#513f868c285963fd2f2dbf54ed7840a2dc05e33a" - integrity sha512-+bbQ6/FN7ryCDdsuyheIPeRa5MO8mTDUDZusNIU97Q8fdmw1hB+eiy9fNThdGfCENd/GPANNsXe6K5olUX7QhQ== +"@cornerstonejs/core@^0.43.1": + version "0.43.1" + resolved "https://registry.npmjs.org/@cornerstonejs/core/-/core-0.43.1.tgz#b51e3310156136e4407d56b1be9fc981022ae4dd" + integrity sha512-TT2EZHWFblkwYnMqiUWYCwtwzWEseXy819YnquWU8OzzsF14k/2JAQPvw8FB0ephv/LoVyXZPC/zARA6U30weg== dependencies: - "@cornerstonejs/core" "^0.40.0" + detect-gpu "^4.0.45" + lodash.clonedeep "4.5.0" + +"@cornerstonejs/streaming-image-volume-loader@^0.16.2": + version "0.16.2" + resolved "https://registry.npmjs.org/@cornerstonejs/streaming-image-volume-loader/-/streaming-image-volume-loader-0.16.2.tgz#7ac513a21d4d8045047a7aa2fb57b5a85682c036" + integrity sha512-2FT0uyuj6+sarAFAdLjd3mGEeW4vD3OPMd/bJltJNyf0eJn0YRC6ke0PwEJj1uyJhEjbhquxsMqhGQIUN8vzpg== + dependencies: + "@cornerstonejs/core" "^0.41.0" cornerstone-wado-image-loader "^4.10.2" -"@cornerstonejs/tools@^0.61.11": - version "0.61.11" - resolved "https://registry.yarnpkg.com/@cornerstonejs/tools/-/tools-0.61.11.tgz#dacd85967cd6ab22c27dd44c10b14664863631f9" - integrity sha512-TCUde2gmuyiyd0EXhoT4DhDZBHYy82MOiekGQe+IG24um3a7GNGJ7jOKBk7fVFxJCTAI2Cb6XI8K79h6BhuWdg== +"@cornerstonejs/tools@^0.63.2": + version "0.63.3" + resolved "https://registry.npmjs.org/@cornerstonejs/tools/-/tools-0.63.3.tgz#a66df8e8a3dc0c1bd5224d85db5d2231ab946f12" + integrity sha512-cgs/6OYcp3p+RSEOb77gR61eziTfb6Y0uK/GrdpgEet3InhFohJCst1TI8rbrHJd4wUX2VDzXHIm5gf6TlwRsA== dependencies: - "@cornerstonejs/core" "^0.42.2" + "@cornerstonejs/core" "^0.43.1" lodash.clonedeep "4.5.0" lodash.get "^4.4.2" @@ -6446,6 +6454,11 @@ array-union@^2.1.0: resolved "https://registry.npmjs.org/array-union/-/array-union-2.1.0.tgz#b798420adbeb1de828d84acd8a2e23d3efe85e8d" integrity sha512-HGyxoOTYUyCM6stUe6EJgnd4EoewAI7zMdfqO+kGjnlZmBDz/cR5pf8r/cR4Wq60sL/p0IkcjUEEPwS3GFrIyw== +array-union@^3.0.1: + version "3.0.1" + resolved "https://registry.npmjs.org/array-union/-/array-union-3.0.1.tgz#da52630d327f8b88cfbfb57728e2af5cd9b6b975" + integrity sha512-1OvF9IbWwaeiM9VhzYXVQacMibxpXOMYVNIvMtKRyX9SImBXpKcFr8XvFDeEslCyuH/t6KRt7HEO94AlP8Iatw== + array-uniq@^1.0.1: version "1.0.3" resolved "https://registry.npmjs.org/array-uniq/-/array-uniq-1.0.3.tgz#af6ac877a25cc7f74e058894753858dfdb24fdb6" @@ -8458,6 +8471,18 @@ copy-text-to-clipboard@^3.0.1: resolved "https://registry.npmjs.org/copy-text-to-clipboard/-/copy-text-to-clipboard-3.0.1.tgz#8cbf8f90e0a47f12e4a24743736265d157bce69c" integrity sha512-rvVsHrpFcL4F2P8ihsoLdFHmd404+CMg71S756oRSeQgqk51U3kicGdnvfkrxva0xXH92SjGS62B0XIJsbh+9Q== +copy-webpack-plugin@^10.2.0: + version "10.2.4" + resolved "https://registry.npmjs.org/copy-webpack-plugin/-/copy-webpack-plugin-10.2.4.tgz#6c854be3fdaae22025da34b9112ccf81c63308fe" + integrity sha512-xFVltahqlsRcyyJqQbDY6EYTtyQZF9rf+JPjwHObLdPFMEISqkFkr7mFoVOC6BfYS/dNThyoQKvziugm+OnwBg== + dependencies: + fast-glob "^3.2.7" + glob-parent "^6.0.1" + globby "^12.0.2" + normalize-path "^3.0.0" + schema-utils "^4.0.0" + serialize-javascript "^6.0.0" + copy-webpack-plugin@^11.0.0: version "11.0.0" resolved "https://registry.npmjs.org/copy-webpack-plugin/-/copy-webpack-plugin-11.0.0.tgz#96d4dbdb5f73d02dd72d0528d1958721ab72e04a" @@ -11996,6 +12021,18 @@ globby@^11.0.1, globby@^11.0.2, globby@^11.0.3, globby@^11.0.4, globby@^11.1.0: merge2 "^1.4.1" slash "^3.0.0" +globby@^12.0.2: + version "12.2.0" + resolved "https://registry.npmjs.org/globby/-/globby-12.2.0.tgz#2ab8046b4fba4ff6eede835b29f678f90e3d3c22" + integrity sha512-wiSuFQLZ+urS9x2gGPl1H5drc5twabmm4m2gTR27XDFyjUHJUNsS8o/2aKyIF6IoBaR630atdher0XJ5g6OMmA== + dependencies: + array-union "^3.0.1" + dir-glob "^3.0.1" + fast-glob "^3.2.7" + ignore "^5.1.9" + merge2 "^1.4.1" + slash "^4.0.0" + globby@^13.1.1: version "13.1.3" resolved "https://registry.npmjs.org/globby/-/globby-13.1.3.tgz#f62baf5720bcb2c1330c8d4ef222ee12318563ff" @@ -12728,7 +12765,7 @@ ignore@^4.0.3, ignore@^4.0.6: resolved "https://registry.npmjs.org/ignore/-/ignore-4.0.6.tgz#750e3db5862087b4737ebac8207ffd1ef27b25fc" integrity sha512-cyFDKrqc/YdcWFniJhzI42+AzS+gNwmUzOSFcRCQYwySuBBBy/KjuxWLZ/FHEH6Moq1NizMOBWyTcv8O4OZIMg== -ignore@^5.0.0, ignore@^5.1.1, ignore@^5.1.8, ignore@^5.2.0: +ignore@^5.0.0, ignore@^5.1.1, ignore@^5.1.8, ignore@^5.1.9, ignore@^5.2.0: version "5.2.4" resolved "https://registry.npmjs.org/ignore/-/ignore-5.2.4.tgz#a291c0c6178ff1b960befe47fcdec301674a6324" integrity sha512-MAb38BcSbH0eHNBxn7ql2NH/kX33OkB3lZ1BNdh7ENeRChHTYsTvWrMubiIAMNS2llXEEgZ1MUOBtXChP3kaFQ== From eea0ed487b06012fdd47d70776fd2cf0e96ed310 Mon Sep 17 00:00:00 2001 From: Alireza Date: Wed, 26 Apr 2023 20:55:56 -0400 Subject: [PATCH 15/54] feat(dicomImageLoader): replace wado image loader with the new library (#3339) * use new dicom image loader instead of cswil new dicom image loader fails update dicom image loader update yarn lock modify webpack * update webpack * fix webpack * update package versions * update package versions --- .webpack/webpack.base.js | 4 +- extensions/cornerstone-dicom-sr/package.json | 2 +- extensions/cornerstone/package.json | 10 +- .../cornerstone/src/initWADOImageLoader.js | 14 +-- .../src/utils/dicomLoaderService.js | 4 +- .../getStudiesForPatientByStudyInstanceUID.js | 2 +- extensions/measurement-tracking/package.json | 2 +- .../getStudiesForPatientByStudyInstanceUID.js | 2 +- platform/core/package.json | 6 +- platform/core/src/classes/MetadataProvider.js | 8 +- platform/viewer/.webpack/webpack.pwa.js | 2 +- platform/viewer/package.json | 6 +- .../src/routes/Local/dicomFileLoader.js | 4 +- .../src/routes/Local/fileLoaderService.js | 4 +- .../viewer/src/routes/Local/pdfFileLoader.js | 4 +- yarn.lock | 99 +++++++------------ 16 files changed, 80 insertions(+), 93 deletions(-) diff --git a/.webpack/webpack.base.js b/.webpack/webpack.base.js index 700e9e1b3..d7e7326c5 100644 --- a/.webpack/webpack.base.js +++ b/.webpack/webpack.base.js @@ -103,8 +103,8 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => { '@hooks': path.resolve(__dirname, '../platform/viewer/src/hooks'), '@routes': path.resolve(__dirname, '../platform/viewer/src/routes'), '@state': path.resolve(__dirname, '../platform/viewer/src/state'), - 'cornerstone-wado-image-loader': - 'cornerstone-wado-image-loader/dist/dynamic-import/cornerstoneWADOImageLoader.min.js', + '@cornerstonejs/dicom-image-loader': + '@cornerstonejs/dicom-image-loader/dist/dynamic-import/cornerstoneDICOMImageLoader.min.js', }, // Which directories to search when resolving modules modules: [ diff --git a/extensions/cornerstone-dicom-sr/package.json b/extensions/cornerstone-dicom-sr/package.json index 34aa3e523..e256b049b 100644 --- a/extensions/cornerstone-dicom-sr/package.json +++ b/extensions/cornerstone-dicom-sr/package.json @@ -47,6 +47,6 @@ "classnames": "^2.3.2", "@cornerstonejs/adapters": "^0.6.0", "@cornerstonejs/core": "^0.42.2", - "@cornerstonejs/tools": "^0.63.2" + "@cornerstonejs/tools": "^0.65.0" } } diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json index d6a6a3ee1..153b15ac8 100644 --- a/extensions/cornerstone/package.json +++ b/extensions/cornerstone/package.json @@ -34,7 +34,11 @@ "peerDependencies": { "@ohif/core": "^3.0.0", "@ohif/ui": "^2.0.0", - "cornerstone-wado-image-loader": "^4.13.0", + "@cornerstonejs/dicom-image-loader": "^0.4.0", + "@cornerstonejs/codec-charls": "^1.2.3", + "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2", + "@cornerstonejs/codec-openjpeg": "^1.2.2", + "@cornerstonejs/codec-openjph": "^2.4.2", "dcmjs": "^0.29.5", "dicom-parser": "^1.8.9", "hammerjs": "^2.0.8", @@ -50,8 +54,8 @@ "@babel/runtime": "^7.20.13", "@cornerstonejs/adapters": "^0.6.0", "@cornerstonejs/core": "^0.42.2", - "@cornerstonejs/streaming-image-volume-loader": "^0.16.2", - "@cornerstonejs/tools": "^0.63.2", + "@cornerstonejs/streaming-image-volume-loader": "^0.18.0", + "@cornerstonejs/tools": "^0.65.0", "@kitware/vtk.js": "26.5.6", "html2canvas": "^1.4.1", "lodash.debounce": "4.0.8", diff --git a/extensions/cornerstone/src/initWADOImageLoader.js b/extensions/cornerstone/src/initWADOImageLoader.js index c072184ee..fbbf3b95d 100644 --- a/extensions/cornerstone/src/initWADOImageLoader.js +++ b/extensions/cornerstone/src/initWADOImageLoader.js @@ -1,9 +1,9 @@ import * as cornerstone from '@cornerstonejs/core'; import { volumeLoader } from '@cornerstonejs/core'; import { cornerstoneStreamingImageVolumeLoader } from '@cornerstonejs/streaming-image-volume-loader'; -import cornerstoneWADOImageLoader, { +import dicomImageLoader, { webWorkerManager, -} from 'cornerstone-wado-image-loader'; +} from '@cornerstonejs/dicom-image-loader'; import dicomParser from 'dicom-parser'; import { errorHandler } from '@ohif/core'; @@ -28,7 +28,7 @@ function initWebWorkers(appConfig) { }; if (!initialized) { - cornerstoneWADOImageLoader.webWorkerManager.initialize(config); + dicomImageLoader.webWorkerManager.initialize(config); initialized = true; } } @@ -37,18 +37,18 @@ export default function initWADOImageLoader( userAuthenticationService, appConfig ) { - cornerstoneWADOImageLoader.external.cornerstone = cornerstone; - cornerstoneWADOImageLoader.external.dicomParser = dicomParser; + dicomImageLoader.external.cornerstone = cornerstone; + dicomImageLoader.external.dicomParser = dicomParser; registerVolumeLoader( 'cornerstoneStreamingImageVolume', cornerstoneStreamingImageVolumeLoader ); - cornerstoneWADOImageLoader.configure({ + dicomImageLoader.configure({ decodeConfig: { // !! IMPORTANT !! - // We should set this flag to false, since, by default cornerstone-wado-image-loader + // We should set this flag to false, since, by default @cornerstonejs/dicom-image-loader // will convert everything to integers (to be able to work with cornerstone-2d). // Until the default is set to true (which is the case for cornerstone3D), // we should set this flag to false. diff --git a/extensions/cornerstone/src/utils/dicomLoaderService.js b/extensions/cornerstone/src/utils/dicomLoaderService.js index 54836fc12..4faaa0e6f 100644 --- a/extensions/cornerstone/src/utils/dicomLoaderService.js +++ b/extensions/cornerstone/src/utils/dicomLoaderService.js @@ -1,5 +1,5 @@ import { imageLoader } from '@cornerstonejs/core'; -import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader'; +import dicomImageLoader from '@cornerstonejs/dicom-image-loader'; import { api } from 'dicomweb-client'; import { DICOMWeb, errorHandler } from '@ohif/core'; @@ -114,7 +114,7 @@ class DicomLoaderService { } if (!someInvalidStrings(imageId)) { - return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId); + return dicomImageLoader.wadouri.loadFileRequest(imageId); } } diff --git a/extensions/default/src/Panels/getStudiesForPatientByStudyInstanceUID.js b/extensions/default/src/Panels/getStudiesForPatientByStudyInstanceUID.js index fb5baa539..e12244885 100644 --- a/extensions/default/src/Panels/getStudiesForPatientByStudyInstanceUID.js +++ b/extensions/default/src/Panels/getStudiesForPatientByStudyInstanceUID.js @@ -8,7 +8,7 @@ async function getStudiesForPatientByStudyInstanceUID( // TODO: The `DicomMetadataStore` should short-circuit both of these requests // Data _could_ be here from route query, or if using JSON data source // We could also force this to "await" these values being available in the DICOMStore? - // Kind of like promise fulfillment in cornerstone-wado-image-loader when there are multiple + // Kind of like promise fulfillment in @cornerstonejs/dicom-image-loader when there are multiple // outgoing requests for the same data const getStudyResult = await dataSource.query.studies.search({ studyInstanceUid: StudyInstanceUID, diff --git a/extensions/measurement-tracking/package.json b/extensions/measurement-tracking/package.json index a695b0268..00aaa9836 100644 --- a/extensions/measurement-tracking/package.json +++ b/extensions/measurement-tracking/package.json @@ -33,7 +33,7 @@ "@ohif/core": "^3.0.0", "classnames": "^2.3.2", "@cornerstonejs/core": "^0.42.2", - "@cornerstonejs/tools": "^0.63.2", + "@cornerstonejs/tools": "^0.65.0", "@ohif/extension-cornerstone-dicom-sr": "^3.0.0", "dcmjs": "^0.29.5", "lodash.debounce": "^4.17.21", diff --git a/extensions/tmtv/src/utils/getStudiesForPatientByStudyInstanceUID.js b/extensions/tmtv/src/utils/getStudiesForPatientByStudyInstanceUID.js index fb5baa539..e12244885 100644 --- a/extensions/tmtv/src/utils/getStudiesForPatientByStudyInstanceUID.js +++ b/extensions/tmtv/src/utils/getStudiesForPatientByStudyInstanceUID.js @@ -8,7 +8,7 @@ async function getStudiesForPatientByStudyInstanceUID( // TODO: The `DicomMetadataStore` should short-circuit both of these requests // Data _could_ be here from route query, or if using JSON data source // We could also force this to "await" these values being available in the DICOMStore? - // Kind of like promise fulfillment in cornerstone-wado-image-loader when there are multiple + // Kind of like promise fulfillment in @cornerstonejs/dicom-image-loader when there are multiple // outgoing requests for the same data const getStudyResult = await dataSource.query.studies.search({ studyInstanceUid: StudyInstanceUID, diff --git a/platform/core/package.json b/platform/core/package.json index afd26b6cb..1bfa7985f 100644 --- a/platform/core/package.json +++ b/platform/core/package.json @@ -32,7 +32,11 @@ }, "peerDependencies": { "cornerstone-math": "0.1.9", - "cornerstone-wado-image-loader": "^4.13.0", + "@cornerstonejs/dicom-image-loader": "^0.4.0", + "@cornerstonejs/codec-charls": "^1.2.3", + "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2", + "@cornerstonejs/codec-openjpeg": "^1.2.2", + "@cornerstonejs/codec-openjph": "^2.4.2", "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 index 02bf2b4e8..159fe169d 100644 --- a/platform/core/src/classes/MetadataProvider.js +++ b/platform/core/src/classes/MetadataProvider.js @@ -116,14 +116,14 @@ class MetadataProvider { return instance[naturalizedTagOrWADOImageLoaderTag]; } - // Maybe its a legacy CornerstoneWADOImageLoader tag then: - return this._getCornerstoneWADOImageLoaderTag( + // Maybe its a legacy dicomImageLoader tag then: + return this._getCornerstoneDICOMImageLoaderTag( naturalizedTagOrWADOImageLoaderTag, instance ); } - _getCornerstoneWADOImageLoaderTag(wadoImageLoaderTag, instance) { + _getCornerstoneDICOMImageLoaderTag(wadoImageLoaderTag, instance) { let metadata; switch (wadoImageLoaderTag) { @@ -496,7 +496,7 @@ const metadataProvider = new MetadataProvider(); export default metadataProvider; const WADO_IMAGE_LOADER_TAGS = { - // CornerstoneWADOImageLoader specific + // dicomImageLoader specific GENERAL_SERIES_MODULE: 'generalSeriesModule', PATIENT_STUDY_MODULE: 'patientStudyModule', IMAGE_PLANE_MODULE: 'imagePlaneModule', diff --git a/platform/viewer/.webpack/webpack.pwa.js b/platform/viewer/.webpack/webpack.pwa.js index 339edbde2..904f3503b 100644 --- a/platform/viewer/.webpack/webpack.pwa.js +++ b/platform/viewer/.webpack/webpack.pwa.js @@ -124,7 +124,7 @@ module.exports = (env, argv) => { patterns: [ { from: - '../../../node_modules/cornerstone-wado-image-loader/dist/dynamic-import', + '../../../node_modules/@cornerstonejs/dicom-image-loader/dist/dynamic-import', to: DIST_DIR, }, ], diff --git a/platform/viewer/package.json b/platform/viewer/package.json index fca0b294c..e8a7bceb8 100644 --- a/platform/viewer/package.json +++ b/platform/viewer/package.json @@ -66,7 +66,11 @@ "config-point": "^0.4.8", "core-js": "^3.16.1", "cornerstone-math": "^0.1.9", - "cornerstone-wado-image-loader": "^4.13.0", + "@cornerstonejs/dicom-image-loader": "^0.4.0", + "@cornerstonejs/codec-charls": "^1.2.3", + "@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2", + "@cornerstonejs/codec-openjpeg": "^1.2.2", + "@cornerstonejs/codec-openjph": "^2.4.2", "dcmjs": "^0.29.5", "detect-gpu": "^4.0.16", "dicom-parser": "^1.8.9", diff --git a/platform/viewer/src/routes/Local/dicomFileLoader.js b/platform/viewer/src/routes/Local/dicomFileLoader.js index 06ef398d3..1188e3169 100644 --- a/platform/viewer/src/routes/Local/dicomFileLoader.js +++ b/platform/viewer/src/routes/Local/dicomFileLoader.js @@ -1,11 +1,11 @@ import dcmjs from 'dcmjs'; -import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader'; +import dicomImageLoader from '@cornerstonejs/dicom-image-loader'; import FileLoader from './fileLoader'; const DICOMFileLoader = new (class extends FileLoader { fileType = 'application/dicom'; loadFile(file, imageId) { - return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId); + return dicomImageLoader.wadouri.loadFileRequest(imageId); } getDataset(image, imageId) { diff --git a/platform/viewer/src/routes/Local/fileLoaderService.js b/platform/viewer/src/routes/Local/fileLoaderService.js index 88a53cef9..9100789a5 100644 --- a/platform/viewer/src/routes/Local/fileLoaderService.js +++ b/platform/viewer/src/routes/Local/fileLoaderService.js @@ -1,4 +1,4 @@ -import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader'; +import dicomImageLoader from '@cornerstonejs/dicom-image-loader'; import FileLoader from './fileLoader'; import PDFFileLoader from './pdfFileLoader'; @@ -15,7 +15,7 @@ class FileLoaderService extends FileLoader { } addFile(file) { - return cornerstoneWADOImageLoader.wadouri.fileManager.add(file); + return dicomImageLoader.wadouri.fileManager.add(file); } loadFile(file, imageId) { diff --git a/platform/viewer/src/routes/Local/pdfFileLoader.js b/platform/viewer/src/routes/Local/pdfFileLoader.js index 6304045ca..6d44d49ba 100644 --- a/platform/viewer/src/routes/Local/pdfFileLoader.js +++ b/platform/viewer/src/routes/Local/pdfFileLoader.js @@ -1,10 +1,10 @@ -import cornerstoneWADOImageLoader from 'cornerstone-wado-image-loader'; +import dicomImageLoader from '@cornerstonejs/dicom-image-loader'; import FileLoader from './fileLoader'; const PDFFileLoader = new (class extends FileLoader { fileType = 'application/pdf'; loadFile(file, imageId) { - return cornerstoneWADOImageLoader.wadouri.loadFileRequest(imageId); + return dicomImageLoader.wadouri.loadFileRequest(imageId); } getDataset(image, imageId) { diff --git a/yarn.lock b/yarn.lock index 032805b51..345d2c627 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1443,44 +1443,53 @@ resolved "https://registry.npmjs.org/@cornerstonejs/codec-openjph/-/codec-openjph-2.4.2.tgz#e96721d56f6ec96f7f95c16321d88cc8467d8d81" integrity sha512-lgdvBvvNezleY+4pIe2ceUsJzlZe/0PipdeubQ3vZZOz3xxtHHMR1XFCl4fgd8gosR8COHuD7h6q+MwgrwBsng== -"@cornerstonejs/core@^0.41.0": - version "0.41.0" - resolved "https://registry.npmjs.org/@cornerstonejs/core/-/core-0.41.0.tgz#1268bc9cb70e101b52e5eee9055a84541d76ef5d" - integrity sha512-Wk4BpDaKYz9KRr6eNiYatxg/ZNsluNN2p5QsK0qNYyquR5ABo/fuBexI160plP3jI4pDKlMH+OpbXuLx3T3ngw== - dependencies: - detect-gpu "^4.0.45" - lodash.clonedeep "4.5.0" - "@cornerstonejs/core@^0.42.2": - version "0.42.2" - resolved "https://registry.yarnpkg.com/@cornerstonejs/core/-/core-0.42.2.tgz#be69adbfd7b63718316a4f18fa55ca473506cee5" - 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version "0.63.3" - resolved "https://registry.npmjs.org/@cornerstonejs/tools/-/tools-0.63.3.tgz#a66df8e8a3dc0c1bd5224d85db5d2231ab946f12" - integrity sha512-cgs/6OYcp3p+RSEOb77gR61eziTfb6Y0uK/GrdpgEet3InhFohJCst1TI8rbrHJd4wUX2VDzXHIm5gf6TlwRsA== +"@cornerstonejs/tools@^0.65.0": + version "0.65.0" + resolved "https://registry.npmjs.org/@cornerstonejs/tools/-/tools-0.65.0.tgz#419800eed71d5c16809b393d5327dfb96b074a32" + integrity sha512-OemuMWJkRx7rvfkhI0QxXC1+3DjREuI1y74vNsyLHk9tOjX6ozbURMAGwoHrUu/Bz+8Xb/n8d6IfAF1CtjaqbA== dependencies: - "@cornerstonejs/core" "^0.43.1" + "@cornerstonejs/core" "^0.44.0" lodash.clonedeep "4.5.0" lodash.get "^4.4.2" @@ -8560,22 +8569,6 @@ cornerstone-wado-image-loader@^4.10.2: pako "^2.0.4" uuid "^9.0.0" -cornerstone-wado-image-loader@^4.13.0: - version "4.13.0" - resolved "https://registry.npmjs.org/cornerstone-wado-image-loader/-/cornerstone-wado-image-loader-4.13.0.tgz#277173973b1d5ec90a2d10557df1f667065953da" - integrity sha512-pv3Ic1wDXUopa3DuSJ/IVmnrdUzEsva8ARB5w/I2JPnH3GaO80yZB6TtCqP8BUf3bl33O15k7EsGSICd2KoeCw== - dependencies: - "@babel/eslint-parser" "^7.19.1" - "@cornerstonejs/codec-charls" "^1.2.3" - "@cornerstonejs/codec-libjpeg-turbo-8bit" "^1.2.2" - "@cornerstonejs/codec-openjpeg" "^1.2.2" - "@cornerstonejs/codec-openjph" "^2.4.2" - coverage-istanbul-loader "^3.0.5" - date-format "^4.0.14" - dicom-parser "^1.8.9" - pako "^2.0.4" - uuid "^9.0.0" - cosmiconfig@^5.0.0, cosmiconfig@^5.1.0, cosmiconfig@^5.2.1: version "5.2.1" resolved "https://registry.npmjs.org/cosmiconfig/-/cosmiconfig-5.2.1.tgz#040f726809c591e77a17c0a3626ca45b4f168b1a" @@ -17927,27 +17920,9 @@ postcss@^7.0.0, postcss@^7.0.1, postcss@^7.0.14, postcss@^7.0.26, postcss@^7.0.2 picocolors "^0.2.1" source-map "^0.6.1" -postcss@^8.2.15, postcss@^8.3.11, postcss@^8.3.5: - version "8.4.14" - resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.14.tgz#ee9274d5622b4858c1007a74d76e42e56fd21caf" - integrity sha512-E398TUmfAYFPBSdzgeieK2Y1+1cpdxJx8yXbK/m57nRhKSmk1GB2tO4lbLBtlkfPQTDKfe4Xqv1ASWPpayPEig== - dependencies: - nanoid "^3.3.4" - picocolors "^1.0.0" - source-map-js "^1.0.2" - -postcss@^8.4.14: - version "8.4.16" - resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.16.tgz#33a1d675fac39941f5f445db0de4db2b6e01d43c" - integrity sha512-ipHE1XBvKzm5xI7hiHCZJCSugxvsdq2mPnsq5+UF+VHCjiBvtDrlxJfMBToWaP9D5XlgNmcFGqoHmUn0EYEaRQ== - dependencies: - nanoid "^3.3.4" - picocolors "^1.0.0" - source-map-js "^1.0.2" - -postcss@^8.4.17, postcss@^8.4.18, postcss@^8.4.19: +postcss@^8.2.15, postcss@^8.3.11, postcss@^8.3.5, postcss@^8.4.14, postcss@^8.4.17, postcss@^8.4.18, postcss@^8.4.19: version "8.4.21" - resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.21.tgz#c639b719a57efc3187b13a1d765675485f4134f4" + resolved "https://registry.npmjs.org/postcss/-/postcss-8.4.21.tgz#c639b719a57efc3187b13a1d765675485f4134f4" integrity sha512-tP7u/Sn/dVxK2NnruI4H9BG+x+Wxz6oeZ1cJ8P6G/PZY0IKk4k/63TDsQf2kQq3+qoJeLm2kIBUNlZe3zgb4Zg== dependencies: nanoid "^3.3.4" @@ -21056,7 +21031,7 @@ table@^6.0.9: tailwindcss@3.2.4: version "3.2.4" - resolved "https://registry.yarnpkg.com/tailwindcss/-/tailwindcss-3.2.4.tgz#afe3477e7a19f3ceafb48e4b083e292ce0dc0250" + resolved "https://registry.npmjs.org/tailwindcss/-/tailwindcss-3.2.4.tgz#afe3477e7a19f3ceafb48e4b083e292ce0dc0250" integrity sha512-AhwtHCKMtR71JgeYDaswmZXhPcW9iuI9Sp2LvZPo9upDZ7231ZJ7eA9RaURbhpXGVlrjX4cFNlB4ieTetEb7hQ== dependencies: arg "^5.0.2" From 51cb0519fcb3090f7427be55af30d2611a245732 Mon Sep 17 00:00:00 2001 From: Joe Boccanfuso <109477394+jbocce@users.noreply.github.com> Date: Thu, 27 Apr 2023 10:46:23 -0400 Subject: [PATCH 16/54] fix(Browser history): fixed NPE when navigating a study via browser history and history navigation is now available via the navigateHistory command (#3337) * fix(Browser history): - fixed an NPE when navigating to a different study via the URL - exposed browser history navigation via a command * Added documentation for the navigateHistory command. Moved the history object from UI to viewer. --- extensions/default/src/commandsModule.ts | 29 +++++++++++++++++ .../default/src/types/commandModuleTypes.tsx | 6 ++++ .../TrackedMeasurementsContext.tsx | 4 +++ platform/docs/docs/platform/modes/routes.md | 31 +++++++++++++++++++ platform/viewer/src/index.js | 4 +++ platform/viewer/src/routes/Mode/Mode.tsx | 6 +++- platform/viewer/src/utils/history.ts | 9 ++++++ 7 files changed, 88 insertions(+), 1 deletion(-) create mode 100644 extensions/default/src/types/commandModuleTypes.tsx create mode 100644 platform/viewer/src/utils/history.ts diff --git a/extensions/default/src/commandsModule.ts b/extensions/default/src/commandsModule.ts index 73b54b5df..172f00921 100644 --- a/extensions/default/src/commandsModule.ts +++ b/extensions/default/src/commandsModule.ts @@ -11,6 +11,8 @@ import findViewportsByPosition, { } from './findViewportsByPosition'; import { ContextMenuProps } from './CustomizeableContextMenu/types'; +import { NavigateHistory } from './types/commandModuleTypes'; +import { history } from '@ohif/viewer'; const { subscribeToNextViewportGridChange } = utils; @@ -480,6 +482,28 @@ const commandsModule = ({ } }, + /** + * Exposes the browser history navigation used by OHIF. This command can be used to either replace or + * push a new entry into the browser history. For example, the following will replace the current + * browser history entry with the specified relative URL which changes the study displayed to the + * study with study instance UID 1.2.3. Note that as a result of using `options.replace = true`, the + * page prior to invoking this command cannot be returned to via the browser back button. + * + * navigateHistory({ + * to: 'viewer?StudyInstanceUIDs=1.2.3', + * options: { replace: true }, + * }); + * + * @param historyArgs - arguments for the history function; + * the `to` property is the URL; + * the `options.replace` is a boolean indicating if the current browser history entry + * should be replaced or a new entry pushed onto the history (stack); the default value + * for `replace` is false + */ + navigateHistory(historyArgs: NavigateHistory) { + history.navigate(historyArgs.to, historyArgs.options); + }, + openDICOMTagViewer() { const { activeViewportIndex, viewports } = viewportGridService.getState(); const activeViewportSpecificData = viewports[activeViewportIndex]; @@ -540,6 +564,11 @@ const commandsModule = ({ storeContexts: [], options: {}, }, + navigateHistory: { + commandFn: actions.navigateHistory, + storeContexts: [], + options: {}, + }, nextStage: { commandFn: actions.deltaStage, storeContexts: [], diff --git a/extensions/default/src/types/commandModuleTypes.tsx b/extensions/default/src/types/commandModuleTypes.tsx new file mode 100644 index 000000000..d2cdde134 --- /dev/null +++ b/extensions/default/src/types/commandModuleTypes.tsx @@ -0,0 +1,6 @@ +export type NavigateHistory = { + to: string; // the URL to navigate to + options?: { + replace?: boolean; // replace or add/push to history? + }; +}; diff --git a/extensions/measurement-tracking/src/contexts/TrackedMeasurementsContext/TrackedMeasurementsContext.tsx b/extensions/measurement-tracking/src/contexts/TrackedMeasurementsContext/TrackedMeasurementsContext.tsx index 476e80a40..f73707220 100644 --- a/extensions/measurement-tracking/src/contexts/TrackedMeasurementsContext/TrackedMeasurementsContext.tsx +++ b/extensions/measurement-tracking/src/contexts/TrackedMeasurementsContext/TrackedMeasurementsContext.tsx @@ -149,6 +149,10 @@ function TrackedMeasurementsContextProvider( activeViewport.displaySetInstanceUIDs[0] ); + if (!displaySet) { + return; + } + // If this is an SR produced by our SR SOPClassHandler, // and it hasn't been loaded yet, do that now so we // can check if it can be rehydrated or not. diff --git a/platform/docs/docs/platform/modes/routes.md b/platform/docs/docs/platform/modes/routes.md index 6e8647309..36376a131 100644 --- a/platform/docs/docs/platform/modes/routes.md +++ b/platform/docs/docs/platform/modes/routes.md @@ -313,3 +313,34 @@ function modeFactory() { }; } ``` + +> How can I navigate to (or show) a different study via the browser history/URL? + +There is a command that does this: `navigateHistory`. It takes an object +argument with the `NavigateHistory` type: + +``` +export type NavigateHistory = { + to: string; // the URL to navigate to + options?: { + replace?: boolean; // replace or add/push to history? + }; +}; +``` + +For instance one could bind a hot key to this command to show a specific study +like this... + +``` + { + commandName: 'navigateHistory', + commandOptions: { + to: + '/viewer?StudyInstanceUIDs=1.2.3', + }, + context: 'DEFAULT', + label: 'Nav Study', + keys: ['n'], + isEditable: true, + }, +``` diff --git a/platform/viewer/src/index.js b/platform/viewer/src/index.js index 49f47fa79..6cec78ad2 100644 --- a/platform/viewer/src/index.js +++ b/platform/viewer/src/index.js @@ -5,6 +5,8 @@ import 'regenerator-runtime/runtime'; import App from './App'; import React from 'react'; import ReactDOM from 'react-dom'; +import { history } from './utils/history'; + /** * EXTENSIONS AND MODES * ================= @@ -34,3 +36,5 @@ loadDynamicImports().then(() => { ReactDOM.render(app, document.getElementById('root')); }); }); + +export { history }; diff --git a/platform/viewer/src/routes/Mode/Mode.tsx b/platform/viewer/src/routes/Mode/Mode.tsx index 7b06bf445..7e7575bc0 100644 --- a/platform/viewer/src/routes/Mode/Mode.tsx +++ b/platform/viewer/src/routes/Mode/Mode.tsx @@ -1,5 +1,5 @@ import React, { useEffect, useState, useRef } from 'react'; -import { useParams, useLocation } from 'react-router'; +import { useParams, useLocation, useNavigate } from 'react-router'; import PropTypes from 'prop-types'; // TODO: DicomMetadataStore should be injected? import { DicomMetadataStore, ServicesManager, utils } from '@ohif/core'; @@ -8,6 +8,7 @@ import { useQuery, useSearchParams } from '@hooks'; import ViewportGrid from '@components/ViewportGrid'; import Compose from './Compose'; import getStudies from './studiesList'; +import { history } from '../../utils/history'; const { getSplitParam } = utils; @@ -105,6 +106,9 @@ export default function ModeRoute({ const locationRef = useRef(null); const isMounted = useRef(false); + // Expose the react router dom navigation. + history.navigate = useNavigate(); + if (location !== locationRef.current) { layoutTemplateData.current = null; locationRef.current = location; diff --git a/platform/viewer/src/utils/history.ts b/platform/viewer/src/utils/history.ts new file mode 100644 index 000000000..57cdf7d35 --- /dev/null +++ b/platform/viewer/src/utils/history.ts @@ -0,0 +1,9 @@ +import { NavigateFunction } from 'react-router'; + +type History = { + navigate: NavigateFunction; +}; + +export const history: History = { + navigate: null, +}; From dd3944a87c1ed8ecb08aa9ea61d1e1592812e5de Mon Sep 17 00:00:00 2001 From: Alireza Date: Thu, 27 Apr 2023 12:13:27 -0400 Subject: [PATCH 17/54] feat(storybook): Refactor Storybook to use Typescript (#3341) * feat(storybook): Refactor Storybook to use Typescript This commit updates the Storybook configuration to use Typescript, including renaming `main.js` to `main.ts`, updating `core.builder` and `framework.name` to use `@storybook/builder-webpack5` and `@storybook/react-webpack5`, respectively. The code also adds options to `addon-docs` to enable adding GFM support to the generated docs. Additionally, the commit modifies `staticDir`, removes outdated addons, and makes various devDependencies and PostCSS updates to align with Storybook 7.x.x. Finally, the commit removes some unused code and relocates `Button` and `AboutModal` story files. * apply review comments * update yarn lock --- platform/ui/.storybook/{main.js => main.ts} | 32 +- platform/ui/.storybook/manager.js | 6 +- platform/ui/.storybook/preview.tsx | 6 +- platform/ui/package.json | 43 +- .../__stories__/aboutModal.stories.mdx | 2 +- .../Button/__stories__/button.stories.mdx | 2 - .../storybook/components/heading/heading.tsx | 4 +- platform/ui/tailwind.config.js | 4 +- yarn.lock | 6475 ++++++++--------- 9 files changed, 3007 insertions(+), 3567 deletions(-) rename platform/ui/.storybook/{main.js => main.ts} (71%) diff --git a/platform/ui/.storybook/main.js b/platform/ui/.storybook/main.ts similarity index 71% rename from platform/ui/.storybook/main.js rename to platform/ui/.storybook/main.ts index 399f439b4..5bed58d84 100644 --- a/platform/ui/.storybook/main.js +++ b/platform/ui/.storybook/main.ts @@ -1,17 +1,35 @@ -const path = require('path'); +import path from 'path'; +import remarkGfm from 'remark-gfm'; +import type { StorybookConfig } from '@storybook/react-webpack5'; -module.exports = { +const config: StorybookConfig = { stories: ['../src/**/*.stories.@(mdx)'], addons: [ '@storybook/addon-links', '@storybook/addon-essentials', - '@storybook/addon-google-analytics', + // Other addons go here + { + name: '@storybook/addon-docs', + options: { + mdxPluginOptions: { + mdxCompileOptions: { + remarkPlugins: [remarkGfm], + }, + }, + }, + }, ], - core: { - builder: 'webpack5', + core: { builder: '@storybook/builder-webpack5' }, + framework: { + name: '@storybook/react-webpack5', + options: {}, + }, + docs: { + autodocs: true, // see below for alternatives + defaultName: 'Docs', // set to change the name of generated docs entries }, staticDirs: ['../static'], - webpackFinal: async (config, { configType }) => { + webpackFinal: async (config: any, { configType }) => { // `configType` has a value of 'DEVELOPMENT' or 'PRODUCTION' // You can change the configuration based on that. // 'PRODUCTION' is used when building the static version of storybook. @@ -73,3 +91,5 @@ module.exports = { return config; }, }; + +export default config; diff --git a/platform/ui/.storybook/manager.js b/platform/ui/.storybook/manager.js index 56d081c23..8ca5f1061 100644 --- a/platform/ui/.storybook/manager.js +++ b/platform/ui/.storybook/manager.js @@ -2,16 +2,14 @@ import { addons } from '@storybook/addons'; import ohifTheme from './OHIFTheme'; -import favicon from '/static/favicon.png'; const link = document.createElement('link'); link.setAttribute('rel', 'shortcut icon'); -link.setAttribute('href', favicon); document.head.appendChild(link); addons.setConfig({ theme: ohifTheme, }); -window.STORYBOOK_GA_ID = "G-3S63CTHNP6" -window.STORYBOOK_REACT_GA_OPTIONS = {} +window.STORYBOOK_GA_ID = 'G-3S63CTHNP6'; +window.STORYBOOK_REACT_GA_OPTIONS = {}; diff --git a/platform/ui/.storybook/preview.tsx b/platform/ui/.storybook/preview.tsx index 111a3276c..1488f8360 100644 --- a/platform/ui/.storybook/preview.tsx +++ b/platform/ui/.storybook/preview.tsx @@ -1,5 +1,4 @@ import React from 'react'; -import { addParameters } from '@storybook/react'; import { DocsPage, DocsContainer } from '@storybook/addon-docs'; import { Heading, @@ -13,7 +12,8 @@ import '../src/tailwind.css'; import './custom.css'; // https://github.com/mondaycom/monday-ui-react-core/tree/master/.storybook -addParameters({ + +export const parameters = { docs: { inlineStories: true, container: ({ children, context }) => ( @@ -78,6 +78,6 @@ addParameters({ order: ['Welcome', 'Contribute', 'Foundations', 'Modals', '*'], }, }, -}); +}; export const decorators = []; diff --git a/platform/ui/package.json b/platform/ui/package.json index 68d73cd20..7862f871f 100644 --- a/platform/ui/package.json +++ b/platform/ui/package.json @@ -22,8 +22,9 @@ "start": "yarn run build --watch", "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js", "build:package": "yarn run build", - "storybook": "start-storybook -p 6006", - "build-storybook": "build-storybook" + "storybook": "storybook dev -p 6006", + "dev": "storybook dev -p 6006", + "build-storybook": "storybook build" }, "peerDependencies": { "react": "17.0.2", @@ -35,6 +36,8 @@ "lodash.debounce": "4.0.8", "moment": "2.24.0", "mousetrap": "^1.6.5", + "react": "^17.0.2", + "react-dom": "^17.0.2", "react-dates": "^21.8.0", "react-dnd": "14.0.2", "react-dnd-html5-backend": "14.0.0", @@ -44,25 +47,27 @@ "react-outside-click-handler": "^1.3.0", "react-select": "3.0.8", "react-with-direction": "^1.3.1", - "swiper": "^8.4.2" + "swiper": "^8.4.2", + "webpack": "^5.81.0" }, "devDependencies": { - "@babel/core": "^7.14.8", - "@storybook/addon-actions": "^6.4.9", - "@storybook/addon-docs": "^6.4.9", - "@storybook/addon-essentials": "^6.4.9", - "@storybook/addon-google-analytics": "^6.2.9", - "@storybook/addon-links": "^6.4.9", - "@storybook/builder-webpack5": "^6.4.9", - "@storybook/manager-webpack5": "^6.4.9", - "@storybook/react": "^6.4.9", - "@storybook/source-loader": "^6.4.9", - "autoprefixer": ">=9.7.4", - "babel-loader": "^8.2.2", - "dotenv-webpack": "6.0.4", - "postcss": "^8.3.5", - "postcss-loader": "^6.1.1", - "prop-types": "15.7.2", + "@babel/core": "^7.21.4", + "@storybook/addon-actions": "^7.0.7", + "@storybook/addon-docs": "^7.0.7", + "@storybook/addon-essentials": "^7.0.7", + "@storybook/addon-links": "^7.0.7", + "@storybook/react": "^7.0.7", + "@storybook/react-webpack5": "^7.0.7", + "@storybook/source-loader": "^7.0.7", + "@storybook/cli": "^7.0.7", + "autoprefixer": "^10.4.14", + "babel-loader": "^9.1.2", + "dotenv-webpack": "^8.0.1", + "postcss": "^8.4.23", + "postcss-loader": "^7.2.4", + "prop-types": "^15.8.1", + "storybook": "^7.0.7", + "remark-gfm": "^3.0.1", "tailwindcss": "3.2.4" } } diff --git a/platform/ui/src/components/AboutModal/__stories__/aboutModal.stories.mdx b/platform/ui/src/components/AboutModal/__stories__/aboutModal.stories.mdx index 3e5127be6..1bd027a6d 100644 --- a/platform/ui/src/components/AboutModal/__stories__/aboutModal.stories.mdx +++ b/platform/ui/src/components/AboutModal/__stories__/aboutModal.stories.mdx @@ -1,4 +1,4 @@ -import AboutModal from '../AboutModal'; +import AboutModal from '../../AboutModal'; import { ArgsTable, Story, Canvas, Meta } from '@storybook/addon-docs'; import { createComponentTemplate, diff --git a/platform/ui/src/components/Button/__stories__/button.stories.mdx b/platform/ui/src/components/Button/__stories__/button.stories.mdx index bb62b5927..e01f38d64 100644 --- a/platform/ui/src/components/Button/__stories__/button.stories.mdx +++ b/platform/ui/src/components/Button/__stories__/button.stories.mdx @@ -123,7 +123,6 @@ You can add an icon to the start of the button. It accepts an icon component. }; return ; }} - }} @@ -157,7 +156,6 @@ End Icon is the same as start icon, but for the end of the button. ); }} - }} diff --git a/platform/ui/src/storybook/components/heading/heading.tsx b/platform/ui/src/storybook/components/heading/heading.tsx index 95059bb8f..d4ff4118a 100644 --- a/platform/ui/src/storybook/components/heading/heading.tsx +++ b/platform/ui/src/storybook/components/heading/heading.tsx @@ -23,14 +23,14 @@ function GitHubLogo() { export const Heading = ({ title, componentRelativePath }) => { return ( -
+

{title}

{componentRelativePath && ( -
+
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sha512-V50KMwwzqJV0NpZIZFwfOD5/lyny3WlSzRiXgA0G7VUnRlqttta1L6UQIHzd6EuBY/cHGfwTIck7w1yH6Q5zUw== + +zwitch@^2.0.0: + version "2.0.4" + resolved "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz#c827d4b0acb76fc3e685a4c6ec2902d51070e9d7" + integrity sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A== From 075008c67452640fc11ada6ac3702e5f9ad53cc8 Mon Sep 17 00:00:00 2001 From: "M.D" <26860200+md-prog@users.noreply.github.com> Date: Thu, 27 Apr 2023 20:53:52 -0400 Subject: [PATCH 18/54] feat(microscopy): add dicom microscopy extension and mode (#3247) * skeleton for dicom-microscopy extension * skeleton for microscopy mode * [feat] ported @radicalimaging/microscopy-dicom to OHIF's default extension * [feat] ported microscopy mode from private repo * added new definitions to the package.json * webpack configuration update for microscopy extension * register new icons for microscopy tools * fixes to the microscopy extension and mode * trivial error fix - typescript type import error * link microscopy extension with default OHIF app plugin config * demo config fix * fix logs * remove unsed imports * [fix] loading of microscopy * [fix] webworker script loading, normalizing denaturalized dataset * found the latest version of dicom-microscopy-viewer that works with current OHIF extension : 0.35.2 * hide thumbnail pane by default, as we have issues with * comments * remove unused code * [feat] microscopy - annotation selection * [feat] microscopy - edit annotation label * wip * [bugfix] dicom-microscopy tool * [bugfix] dicom microscopy annotations * [fix] mixed-content blocking caused by BulkDataURI * [fix] microscopy measurements panel - center button * [fix] microscopy measurements panel - styling * [fix] microscopy - controls * fix local loading of microscopy * fix local loading of dicom microscopy * fix typo - indexof to indexOf * [fix] remove unused icons * remove commented out lines from webpack configuration * platform/viewer/public/config/default.js - revert accidental changes * [refactor] redirecting to microscopy mode on Local mode * attribution to DMV and SLIM viewer * [fix] code review feedbacks * fix thumbnails * [fix] microscopy - fix old publisher.publish() to PubSubService._broadcastEvent() * [fix] interactions, webpack config, roi selection * [feat] microscopy - remove select tool from UI * microscopy author * [fix] saving and loading SR * [bugfix] - missing publish() function in MicroscopyService, replace with _broadcastEvent * remove author section from readme * refactor SR saving feature * fix webpack config after merge * [bugfix] repeated import * fix e2e * webpack configuration * hide "Create report" button for microscopy --- .webpack/rules/transpileJavaScript.js | 2 +- .webpack/webpack.base.js | 7 + extensions/cornerstone/src/index.tsx | 2 +- .../default/src/Panels/PanelStudyBrowser.tsx | 1 + extensions/dicom-microscopy/.gitignore | 104 +++ extensions/dicom-microscopy/.prettierrc | 8 + .../dicom-microscopy/.webpack/webpack.dev.js | 8 + .../dicom-microscopy/.webpack/webpack.prod.js | 63 ++ extensions/dicom-microscopy/LICENSE | 9 + extensions/dicom-microscopy/README.md | 11 + extensions/dicom-microscopy/babel.config.js | 44 ++ extensions/dicom-microscopy/package.json | 79 +++ .../src/DicomMicroscopySRSopClassHandler.js | 143 ++++ .../src/DicomMicroscopySopClassHandler.js | 132 ++++ .../src/DicomMicroscopyViewport.css | 352 ++++++++++ .../src/DicomMicroscopyViewport.tsx | 321 +++++++++ .../MicroscopyPanel/MicroscopyPanel.tsx | 413 ++++++++++++ .../ViewportOverlay/ViewportOverlay.css | 87 +++ .../src/components/ViewportOverlay/index.tsx | 155 +++++ .../listComponentGenerator.tsx | 12 + .../src/components/ViewportOverlay/utils.ts | 102 +++ .../dicom-microscopy/src/getCommandsModule.ts | 198 ++++++ .../dicom-microscopy/src/getPanelModule.tsx | 49 ++ .../src/helpers/formatDICOMDate.js | 11 + .../src/helpers/formatDICOMDate.test.js | 9 + .../src/helpers/formatDICOMPatientName.js | 21 + .../helpers/formatDICOMPatientName.test.js | 17 + .../src/helpers/formatDICOMTime.js | 17 + .../src/helpers/formatDICOMTime.test.js | 9 + .../src/helpers/formatNumberPrecision.js | 9 + .../src/helpers/formatNumberPrecision.test.js | 9 + .../dicom-microscopy/src/helpers/index.js | 15 + .../src/helpers/isValidNumber.js | 3 + extensions/dicom-microscopy/src/id.js | 5 + extensions/dicom-microscopy/src/index.tsx | 117 ++++ .../src/services/MicroscopyService.js | 634 ++++++++++++++++++ .../src/tools/viewerManager.js | 491 ++++++++++++++ .../src/utils/DEVICE_OBSERVER_UID.js | 5 + .../src/utils/RoiAnnotation.js | 196 ++++++ .../src/utils/areaOfPolygon.js | 17 + .../src/utils/callInputDialog.tsx | 75 +++ .../src/utils/cleanDenaturalizedDataset.ts | 63 ++ .../dicom-microscopy/src/utils/constructSR.ts | 213 ++++++ .../coordinateFormatScoord3d2Geometry.js | 110 +++ .../src/utils/dcmCodeValues.js | 14 + .../src/utils/dicomWebClient.ts | 96 +++ .../src/utils/getSourceDisplaySet.js | 38 ++ .../dicom-microscopy/src/utils/loadSR.js | 207 ++++++ .../src/utils/saveByteArray.ts | 12 + .../dicom-microscopy/src/utils/styles.js | 48 ++ .../dicom-microscopy/src/utils/toArray.js | 3 + extensions/dicom-microscopy/tsconfig.json | 11 + .../PanelStudyBrowserTracking.tsx | 1 + modes/microscopy/.gitignore | 104 +++ modes/microscopy/.prettierrc | 8 + modes/microscopy/.webpack/webpack.dev.js | 8 + modes/microscopy/.webpack/webpack.prod.js | 62 ++ modes/microscopy/LICENSE | 9 + modes/microscopy/README.md | 13 + modes/microscopy/babel.config.js | 44 ++ modes/microscopy/package.json | 65 ++ modes/microscopy/src/id.js | 5 + modes/microscopy/src/index.tsx | 142 ++++ modes/microscopy/src/toolbarButtons.js | 184 +++++ .../DicomMetadataStore/createStudyMetadata.js | 2 +- .../core/src/utils/isLowPriorityModality.ts | 8 +- .../assets/icons/tool-freehand-polygon.svg | 37 + .../ui/src/assets/icons/tool-freehand.svg | 34 + platform/ui/src/assets/icons/tool-polygon.svg | 3 + platform/ui/src/components/Icon/getIcon.js | 8 + platform/viewer/.webpack/webpack.pwa.js | 25 +- platform/viewer/package.json | 2 + platform/viewer/pluginConfig.json | 8 + platform/viewer/public/config/demo.js | 16 +- platform/viewer/src/routes/Local/Local.tsx | 35 +- yarn.lock | 299 ++++++++- 76 files changed, 5868 insertions(+), 31 deletions(-) create mode 100644 extensions/dicom-microscopy/.gitignore create mode 100644 extensions/dicom-microscopy/.prettierrc create mode 100644 extensions/dicom-microscopy/.webpack/webpack.dev.js create mode 100644 extensions/dicom-microscopy/.webpack/webpack.prod.js create mode 100644 extensions/dicom-microscopy/LICENSE create mode 100644 extensions/dicom-microscopy/README.md create mode 100644 extensions/dicom-microscopy/babel.config.js create mode 100644 extensions/dicom-microscopy/package.json create mode 100644 extensions/dicom-microscopy/src/DicomMicroscopySRSopClassHandler.js create mode 100644 extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js create mode 100644 extensions/dicom-microscopy/src/DicomMicroscopyViewport.css create mode 100644 extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx create mode 100644 extensions/dicom-microscopy/src/components/MicroscopyPanel/MicroscopyPanel.tsx create mode 100644 extensions/dicom-microscopy/src/components/ViewportOverlay/ViewportOverlay.css create mode 100644 extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx create mode 100644 extensions/dicom-microscopy/src/components/ViewportOverlay/listComponentGenerator.tsx create mode 100644 extensions/dicom-microscopy/src/components/ViewportOverlay/utils.ts create mode 100644 extensions/dicom-microscopy/src/getCommandsModule.ts create mode 100644 extensions/dicom-microscopy/src/getPanelModule.tsx create mode 100644 extensions/dicom-microscopy/src/helpers/formatDICOMDate.js create mode 100644 extensions/dicom-microscopy/src/helpers/formatDICOMDate.test.js create mode 100644 extensions/dicom-microscopy/src/helpers/formatDICOMPatientName.js create mode 100644 extensions/dicom-microscopy/src/helpers/formatDICOMPatientName.test.js create mode 100644 extensions/dicom-microscopy/src/helpers/formatDICOMTime.js create mode 100644 extensions/dicom-microscopy/src/helpers/formatDICOMTime.test.js create mode 100644 extensions/dicom-microscopy/src/helpers/formatNumberPrecision.js create mode 100644 extensions/dicom-microscopy/src/helpers/formatNumberPrecision.test.js create mode 100644 extensions/dicom-microscopy/src/helpers/index.js create mode 100644 extensions/dicom-microscopy/src/helpers/isValidNumber.js create mode 100644 extensions/dicom-microscopy/src/id.js create mode 100644 extensions/dicom-microscopy/src/index.tsx create mode 100644 extensions/dicom-microscopy/src/services/MicroscopyService.js create mode 100644 extensions/dicom-microscopy/src/tools/viewerManager.js create mode 100644 extensions/dicom-microscopy/src/utils/DEVICE_OBSERVER_UID.js create mode 100644 extensions/dicom-microscopy/src/utils/RoiAnnotation.js create mode 100644 extensions/dicom-microscopy/src/utils/areaOfPolygon.js create mode 100644 extensions/dicom-microscopy/src/utils/callInputDialog.tsx create mode 100644 extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts create mode 100644 extensions/dicom-microscopy/src/utils/constructSR.ts create mode 100644 extensions/dicom-microscopy/src/utils/coordinateFormatScoord3d2Geometry.js create mode 100644 extensions/dicom-microscopy/src/utils/dcmCodeValues.js create mode 100644 extensions/dicom-microscopy/src/utils/dicomWebClient.ts create mode 100644 extensions/dicom-microscopy/src/utils/getSourceDisplaySet.js create mode 100644 extensions/dicom-microscopy/src/utils/loadSR.js create mode 100644 extensions/dicom-microscopy/src/utils/saveByteArray.ts create mode 100644 extensions/dicom-microscopy/src/utils/styles.js create mode 100644 extensions/dicom-microscopy/src/utils/toArray.js create mode 100644 extensions/dicom-microscopy/tsconfig.json create mode 100644 modes/microscopy/.gitignore create mode 100644 modes/microscopy/.prettierrc create mode 100644 modes/microscopy/.webpack/webpack.dev.js create mode 100644 modes/microscopy/.webpack/webpack.prod.js create mode 100644 modes/microscopy/LICENSE create mode 100644 modes/microscopy/README.md create mode 100644 modes/microscopy/babel.config.js create mode 100644 modes/microscopy/package.json create mode 100644 modes/microscopy/src/id.js create mode 100644 modes/microscopy/src/index.tsx create mode 100644 modes/microscopy/src/toolbarButtons.js create mode 100644 platform/ui/src/assets/icons/tool-freehand-polygon.svg create mode 100644 platform/ui/src/assets/icons/tool-freehand.svg create mode 100644 platform/ui/src/assets/icons/tool-polygon.svg diff --git a/.webpack/rules/transpileJavaScript.js b/.webpack/rules/transpileJavaScript.js index d576e5839..ca7f00c7a 100644 --- a/.webpack/rules/transpileJavaScript.js +++ b/.webpack/rules/transpileJavaScript.js @@ -25,7 +25,7 @@ function transpileJavaScript(mode) { // These are packages that are not transpiled to our lowest supported // JS version (currently ES5). Most of these leverage ES6+ features, // that we need to transpile to a different syntax. - exclude, + exclude: [/(codecs)/, /(dicomicc)/, exclude], loader: 'babel-loader', options: { // Find babel.config.js in monorepo root diff --git a/.webpack/webpack.base.js b/.webpack/webpack.base.js index d7e7326c5..fa63a45db 100644 --- a/.webpack/webpack.base.js +++ b/.webpack/webpack.base.js @@ -78,6 +78,7 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => { }, }, module: { + noParse: [/(codec)/, /(dicomicc)/], rules: [ transpileJavaScriptRule(mode), loadWebWorkersRule, @@ -89,6 +90,10 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => { }, }, cssToJavaScript, + { + test: /\.wasm/, + type: 'asset/resource', + }, ], //.concat(vtkRules), }, resolve: { @@ -103,6 +108,8 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => { '@hooks': path.resolve(__dirname, '../platform/viewer/src/hooks'), '@routes': path.resolve(__dirname, '../platform/viewer/src/routes'), '@state': path.resolve(__dirname, '../platform/viewer/src/state'), + 'dicom-microscopy-viewer': + 'dicom-microscopy-viewer/dist/dynamic-import/dicomMicroscopyViewer.min.js', '@cornerstonejs/dicom-image-loader': '@cornerstonejs/dicom-image-loader/dist/dynamic-import/cornerstoneDICOMImageLoader.min.js', }, diff --git a/extensions/cornerstone/src/index.tsx b/extensions/cornerstone/src/index.tsx index 643022e15..056c08d5a 100644 --- a/extensions/cornerstone/src/index.tsx +++ b/extensions/cornerstone/src/index.tsx @@ -28,7 +28,7 @@ import { registerColormap } from './utils/colormap/transferFunctionHelpers'; import { id } from './id'; import * as csWADOImageLoader from './initWADOImageLoader.js'; import { measurementMappingUtils } from './utils/measurementServiceMappings'; -import { PublicViewportOptions } from './services/ViewportService/Viewport'; +import type { PublicViewportOptions } from './services/ViewportService/Viewport'; const Component = React.lazy(() => { return import( diff --git a/extensions/default/src/Panels/PanelStudyBrowser.tsx b/extensions/default/src/Panels/PanelStudyBrowser.tsx index 3e7a072cd..8a8244b36 100644 --- a/extensions/default/src/Panels/PanelStudyBrowser.tsx +++ b/extensions/default/src/Panels/PanelStudyBrowser.tsx @@ -321,6 +321,7 @@ function _mapDisplaySets(displaySets, thumbnailImageSrcMap) { const thumbnailNoImageModalities = [ 'SR', 'SEG', + 'SM', 'RTSTRUCT', 'RTPLAN', 'RTDOSE', diff --git a/extensions/dicom-microscopy/.gitignore b/extensions/dicom-microscopy/.gitignore new file mode 100644 index 000000000..67045665d --- /dev/null +++ b/extensions/dicom-microscopy/.gitignore @@ -0,0 +1,104 @@ +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +lerna-debug.log* + +# Diagnostic reports (https://nodejs.org/api/report.html) +report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json + +# Runtime data +pids +*.pid +*.seed +*.pid.lock + +# Directory for instrumented libs generated by jscoverage/JSCover +lib-cov + +# Coverage directory used by tools like istanbul +coverage +*.lcov + +# nyc test coverage +.nyc_output + +# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files) +.grunt + +# Bower dependency directory (https://bower.io/) +bower_components + +# node-waf configuration +.lock-wscript + +# Compiled binary addons (https://nodejs.org/api/addons.html) +build/Release + +# Dependency directories +node_modules/ +jspm_packages/ + +# TypeScript v1 declaration files +typings/ + +# TypeScript cache +*.tsbuildinfo + +# Optional npm cache directory +.npm + +# Optional eslint cache +.eslintcache + +# Microbundle cache +.rpt2_cache/ +.rts2_cache_cjs/ +.rts2_cache_es/ +.rts2_cache_umd/ + +# Optional REPL history +.node_repl_history + +# Output of 'npm pack' +*.tgz + +# Yarn Integrity file +.yarn-integrity + +# dotenv environment variables file +.env +.env.test + +# parcel-bundler cache (https://parceljs.org/) +.cache + +# Next.js build output +.next + +# Nuxt.js build / generate output +.nuxt +dist + +# Gatsby files +.cache/ +# Comment in the public line in if your project uses Gatsby and *not* Next.js +# https://nextjs.org/blog/next-9-1#public-directory-support +# public + +# vuepress build output +.vuepress/dist + +# Serverless directories +.serverless/ + +# FuseBox cache +.fusebox/ + +# DynamoDB Local files +.dynamodb/ + +# TernJS port file +.tern-port diff --git a/extensions/dicom-microscopy/.prettierrc b/extensions/dicom-microscopy/.prettierrc new file mode 100644 index 000000000..b80ec6b34 --- /dev/null +++ b/extensions/dicom-microscopy/.prettierrc @@ -0,0 +1,8 @@ +{ + "trailingComma": "es5", + "printWidth": 80, + "proseWrap": "always", + "tabWidth": 2, + "semi": true, + "singleQuote": true +} diff --git a/extensions/dicom-microscopy/.webpack/webpack.dev.js b/extensions/dicom-microscopy/.webpack/webpack.dev.js new file mode 100644 index 000000000..db7c206b1 --- /dev/null +++ b/extensions/dicom-microscopy/.webpack/webpack.dev.js @@ -0,0 +1,8 @@ +const path = require('path'); +const webpackCommon = require('./../../../.webpack/webpack.base.js'); +const SRC_DIR = path.join(__dirname, '../src'); +const DIST_DIR = path.join(__dirname, '../dist'); + +module.exports = (env, argv) => { + return webpackCommon(env, argv, { SRC_DIR, DIST_DIR }); +}; diff --git a/extensions/dicom-microscopy/.webpack/webpack.prod.js b/extensions/dicom-microscopy/.webpack/webpack.prod.js new file mode 100644 index 000000000..070a723e3 --- /dev/null +++ b/extensions/dicom-microscopy/.webpack/webpack.prod.js @@ -0,0 +1,63 @@ +const path = require('path'); +const pkg = require('../package.json'); + +const outputFile = 'index.umd.js'; +const rootDir = path.resolve(__dirname, '../'); +const outputFolder = path.join(__dirname, `../dist/umd/${pkg.name}/`); + +// Todo: add ESM build for the extension in addition to umd build + +const config = { + mode: 'production', + entry: rootDir + '/' + pkg.module, + devtool: 'source-map', + output: { + path: outputFolder, + filename: outputFile, + library: pkg.name, + libraryTarget: 'umd', + chunkFilename: '[name].chunk.js', + umdNamedDefine: true, + globalObject: "typeof self !== 'undefined' ? self : this", + }, + externals: [ + { + react: { + root: 'React', + commonjs2: 'react', + commonjs: 'react', + amd: 'react', + }, + '@ohif/core': { + commonjs2: '@ohif/core', + commonjs: '@ohif/core', + amd: '@ohif/core', + root: '@ohif/core', + }, + '@ohif/ui': { + commonjs2: '@ohif/ui', + commonjs: '@ohif/ui', + amd: '@ohif/ui', + root: '@ohif/ui', + }, + }, + ], + module: { + rules: [ + { + test: /(\.jsx|\.js|\.tsx|\.ts)$/, + loader: 'babel-loader', + exclude: /(node_modules|bower_components)/, + resolve: { + extensions: ['.js', '.jsx', '.ts', '.tsx'], + }, + }, + ], + }, + resolve: { + modules: [path.resolve('./node_modules'), path.resolve('./src')], + extensions: ['.json', '.js', '.jsx', '.tsx', '.ts'], + }, +}; + +module.exports = config; diff --git a/extensions/dicom-microscopy/LICENSE b/extensions/dicom-microscopy/LICENSE new file mode 100644 index 000000000..effbc2d2f --- /dev/null +++ b/extensions/dicom-microscopy/LICENSE @@ -0,0 +1,9 @@ +MIT License + +Copyright (c) 2023 dicom-microscopy (26860200+md-prog@users.noreply.github.com) + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. \ No newline at end of file diff --git a/extensions/dicom-microscopy/README.md b/extensions/dicom-microscopy/README.md new file mode 100644 index 000000000..cecf00af2 --- /dev/null +++ b/extensions/dicom-microscopy/README.md @@ -0,0 +1,11 @@ +# OHIF extension for microscopy +Adapter for *DICOM Microscopy Viewer* to get it integrated into OHIF Viewer. + +## Acknowledgements + +- [DICOM Microscopy Viewer](https://github.com/ImagingDataCommons/dicom-microscopy-viewer) is a Vanilla JS library for web-based visualization of DICOM VL Whole Slide Microscopy Image datasets and derived information. +- [SLIM Viewer](https://github.com/imagingdatacommons/slim) is a single-page application for interactive visualization and annotation of digital whole slide microscopy images and derived image analysis results in standard DICOM format. The application is based on the dicom-microscopy-viewer JavaScript library and runs fully client side without any custom server components. + + +## License +MIT diff --git a/extensions/dicom-microscopy/babel.config.js b/extensions/dicom-microscopy/babel.config.js new file mode 100644 index 000000000..92fbbdeaf --- /dev/null +++ b/extensions/dicom-microscopy/babel.config.js @@ -0,0 +1,44 @@ +module.exports = { + plugins: ['inline-react-svg', '@babel/plugin-proposal-class-properties'], + env: { + test: { + presets: [ + [ + // TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2 + '@babel/preset-env', + { + modules: 'commonjs', + debug: false, + }, + "@babel/preset-typescript", + ], + '@babel/preset-react', + ], + plugins: [ + '@babel/plugin-proposal-object-rest-spread', + '@babel/plugin-syntax-dynamic-import', + '@babel/plugin-transform-regenerator', + '@babel/plugin-transform-runtime', + ], + }, + production: { + presets: [ + // WebPack handles ES6 --> Target Syntax + ['@babel/preset-env', { modules: false }], + '@babel/preset-react', + "@babel/preset-typescript", + ], + ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'], + }, + development: { + presets: [ + // WebPack handles ES6 --> Target Syntax + ['@babel/preset-env', { modules: false }], + '@babel/preset-react', + "@babel/preset-typescript", + ], + plugins: ['react-hot-loader/babel'], + ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'], + }, + }, +}; diff --git a/extensions/dicom-microscopy/package.json b/extensions/dicom-microscopy/package.json new file mode 100644 index 000000000..d08fd1523 --- /dev/null +++ b/extensions/dicom-microscopy/package.json @@ -0,0 +1,79 @@ +{ + "name": "@ohif/extension-dicom-microscopy", + "version": "3.0.0", + "description": "OHIF extension for DICOM microscopy", + "author": "Bill Wallace, md-prog", + "license": "MIT", + "main": "dist/umd/@ohif/extension-dicom-microscopy/index.umd.js", + "files": [ + "dist/**", + "public/**", + "README.md" + ], + "repository": "OHIF/Viewers", + "keywords": [ + "ohif-extension" + ], + "module": "src/index.tsx", + "engines": { + "node": ">=14", + "npm": ">=6", + "yarn": ">=1.18.0" + }, + "scripts": { + "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo", + "dev:dicom-pdf": "yarn run dev", + "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js", + "build:package": "yarn run build", + "start": "yarn run dev" + }, + "peerDependencies": { + "@ohif/core": "^3.0.0", + "@ohif/extension-default": "^3.0.0", + "@ohif/i18n": "^1.0.0", + "@ohif/ui": "^2.0.0", + "prop-types": "^15.6.2", + "react": "^17.0.2", + "react-dom": "^17.0.2", + "react-i18next": "^10.11.0", + "react-router": "^6.8.1", + "react-router-dom": "^6.8.1", + "webpack": "^5.50.0", + "webpack-merge": "^5.7.3" + }, + "dependencies": { + "@babel/runtime": "^7.20.13", + "@cornerstonejs/codec-charls": "^0.1.1", + "@cornerstonejs/codec-libjpeg-turbo-8bit": "^0.0.7", + "@cornerstonejs/codec-openjpeg": "^0.1.1", + "colormap": "^2.3", + "dicom-microscopy-viewer": "^0.44.0", + "dicomicc": "^0.1" + }, + "devDependencies": { + "@babel/core": "^7.17.8", + "@babel/plugin-proposal-class-properties": "^7.16.7", + "@babel/plugin-proposal-object-rest-spread": "^7.17.3", + "@babel/plugin-proposal-private-methods": "^7.18.6", + "@babel/plugin-syntax-dynamic-import": "^7.8.3", + "@babel/plugin-transform-arrow-functions": "^7.16.7", + "@babel/plugin-transform-regenerator": "^7.16.7", + "@babel/plugin-transform-runtime": "^7.17.0", + "@babel/plugin-transform-typescript": "^7.13.0", + "@babel/preset-env": "^7.16.11", + "@babel/preset-react": "^7.16.7", + "@babel/preset-typescript": "^7.13.0", + "babel-eslint": "^8.0.3", + "babel-loader": "^8.0.0-beta.4", + "babel-plugin-inline-react-svg": "^2.0.1", + "clean-webpack-plugin": "^4.0.0", + "copy-webpack-plugin": "^10.2.0", + "cross-env": "^7.0.3", + "dotenv": "^14.1.0", + "eslint": "^5.0.1", + "eslint-loader": "^2.0.0", + "webpack": "^5.50.0", + "webpack-cli": "^4.7.2", + "webpack-merge": "^5.7.3" + } +} diff --git a/extensions/dicom-microscopy/src/DicomMicroscopySRSopClassHandler.js b/extensions/dicom-microscopy/src/DicomMicroscopySRSopClassHandler.js new file mode 100644 index 000000000..9f5fb3979 --- /dev/null +++ b/extensions/dicom-microscopy/src/DicomMicroscopySRSopClassHandler.js @@ -0,0 +1,143 @@ +import OHIF, { DicomMetadataStore } from '@ohif/core'; +import loadSR from './utils/loadSR'; +import toArray from './utils/toArray'; +import DCM_CODE_VALUES from './utils/dcmCodeValues'; +import getSourceDisplaySet from './utils/getSourceDisplaySet'; + +const { utils } = OHIF; + +const SOP_CLASS_UIDS = { + COMPREHENSIVE_3D_SR: '1.2.840.10008.5.1.4.1.1.88.34', +}; + +const SOPClassHandlerId = + '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySRSopClassHandler'; + +function _getReferencedFrameOfReferenceUID(naturalizedDataset) { + const { ContentSequence } = naturalizedDataset; + + const imagingMeasurementsContentItem = ContentSequence.find( + ci => + ci.ConceptNameCodeSequence.CodeValue === + DCM_CODE_VALUES.IMAGING_MEASUREMENTS + ); + + const firstMeasurementGroupContentItem = toArray( + imagingMeasurementsContentItem.ContentSequence + ).find( + ci => + ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.MEASUREMENT_GROUP + ); + + const imageRegionContentItem = toArray( + firstMeasurementGroupContentItem.ContentSequence + ).find( + ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.IMAGE_REGION + ); + + return imageRegionContentItem.ReferencedFrameOfReferenceUID; +} + +function _getDisplaySetsFromSeries( + instances, + servicesManager, + extensionManager +) { + // If the series has no instances, stop here + if (!instances || !instances.length) { + throw new Error('No instances were provided'); + } + + const { displaySetService, microscopyService } = servicesManager.services; + + const instance = instances[0]; + + // TODO ! Consumption of DICOMMicroscopySRSOPClassHandler to a derived dataset or normal dataset? + // TOOD -> Easy to swap this to a "non-derived" displaySet, but unfortunately need to put it in a different extension. + const naturalizedDataset = DicomMetadataStore.getSeries( + instance.StudyInstanceUID, + instance.SeriesInstanceUID + ).instances[0]; + const ReferencedFrameOfReferenceUID = _getReferencedFrameOfReferenceUID( + naturalizedDataset + ); + + const { + FrameOfReferenceUID, + SeriesDescription, + ContentDate, + ContentTime, + SeriesNumber, + StudyInstanceUID, + SeriesInstanceUID, + SOPInstanceUID, + SOPClassUID, + } = instance; + + const displaySet = { + plugin: 'microscopy', + Modality: 'SR', + altImageText: 'Microscopy SR', + displaySetInstanceUID: utils.guid(), + SOPInstanceUID, + SeriesInstanceUID, + StudyInstanceUID, + ReferencedFrameOfReferenceUID, + SOPClassHandlerId, + SOPClassUID, + SeriesDescription, + // Map the content date/time to the series date/time, these are only used for filtering. + SeriesDate: ContentDate, + SeriesTime: ContentTime, + SeriesNumber, + instance, + metadata: naturalizedDataset, + isDerived: true, + isLoading: false, + isLoaded: false, + loadError: false, + }; + + displaySet.load = function(referencedDisplaySet) { + return loadSR(microscopyService, displaySet, referencedDisplaySet).catch( + error => { + displaySet.isLoaded = false; + displaySet.loadError = true; + throw new Error(error); + } + ); + }; + + displaySet.getSourceDisplaySet = function() { + let allDisplaySets = []; + const studyMetadata = DicomMetadataStore.getStudy(StudyInstanceUID); + studyMetadata.series.forEach(series => { + const displaySets = displaySetService.getDisplaySetsForSeries( + series.SeriesInstanceUID + ); + allDisplaySets = allDisplaySets.concat(displaySets); + }); + return getSourceDisplaySet(allDisplaySets, displaySet); + }; + + return [displaySet]; +} + +export default function getDicomMicroscopySRSopClassHandler({ + servicesManager, + extensionManager, +}) { + const getDisplaySetsFromSeries = instances => { + return _getDisplaySetsFromSeries( + instances, + servicesManager, + extensionManager + ); + }; + + return { + name: 'DicomMicroscopySRSopClassHandler', + sopClassUids: [SOP_CLASS_UIDS.COMPREHENSIVE_3D_SR], + getDisplaySetsFromSeries, + }; +} diff --git a/extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js b/extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js new file mode 100644 index 000000000..d7c6af93e --- /dev/null +++ b/extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js @@ -0,0 +1,132 @@ +import OHIF from '@ohif/core'; + +const { utils } = OHIF; + +const SOP_CLASS_UIDS = { + VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE: '1.2.840.10008.5.1.4.1.1.77.1.6', +}; + +const SOPClassHandlerId = + '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySopClassHandler'; + +function _getDisplaySetsFromSeries( + instances, + servicesManager, + extensionManager +) { + // If the series has no instances, stop here + if (!instances || !instances.length) { + throw new Error('No instances were provided'); + } + + const instance = instances[0]; + + let singleFrameInstance = instance; + let currentFrames = +singleFrameInstance.NumberOfFrames || 1; + for (const instanceI of instances) { + const framesI = +instanceI.NumberOfFrames || 1; + if (framesI < currentFrames) { + singleFrameInstance = instanceI; + currentFrames = framesI; + } + } + let imageIdForThumbnail = null; + if (singleFrameInstance) { + if (currentFrames == 1) { + // Not all DICOM server implementations support thumbnail service, + // So if we have a single-frame image, we will prefer it. + imageIdForThumbnail = singleFrameInstance.imageId; + } + if (!imageIdForThumbnail) { + // use the thumbnail service provided by DICOM server + const dataSource = extensionManager.getActiveDataSource()[0]; + imageIdForThumbnail = dataSource.getImageIdsForInstance({ + instance: singleFrameInstance, + thumbnail: true, + }); + } + } + + const { + FrameOfReferenceUID, + SeriesDescription, + ContentDate, + ContentTime, + SeriesNumber, + StudyInstanceUID, + SeriesInstanceUID, + SOPInstanceUID, + SOPClassUID, + } = instance; + + instances = instances.map(inst => { + // NOTE: According to DICOM standard a series should have a FrameOfReferenceUID + // When the Microscopy file was built by certain tool from multiple image files, + // each instance's FrameOfReferenceUID is sometimes different. + // Even though this means the file was not well formatted DICOM VL Whole Slide Microscopy Image, + // the case is so often, so let's override this value manually here. + // + // https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.7.4.html#sect_C.7.4.1.1.1 + + inst.FrameOfReferenceUID = instance.FrameOfReferenceUID; + + return inst; + }); + + const othersFrameOfReferenceUID = instances + .filter(v => v) + .map(inst => inst.FrameOfReferenceUID) + .filter((value, index, array) => array.indexOf(value) === index); + if (othersFrameOfReferenceUID.length > 1) { + console.warn( + 'Expected FrameOfReferenceUID of difference instances within a series to be the same, found multiple different values', + othersFrameOfReferenceUID + ); + } + + const displaySet = { + plugin: 'microscopy', + Modality: 'SM', + altImageText: 'Microscopy', + displaySetInstanceUID: utils.guid(), + SOPInstanceUID, + SeriesInstanceUID, + StudyInstanceUID, + FrameOfReferenceUID, + SOPClassHandlerId, + SOPClassUID, + SeriesDescription: SeriesDescription || 'Microscopy Data', + // Map ContentDate/Time to SeriesTime for series list sorting. + SeriesDate: ContentDate, + SeriesTime: ContentTime, + SeriesNumber, + firstInstance: singleFrameInstance, // top level instance in the image Pyramid + instance, + numImageFrames: 0, + numInstances: 1, + imageIdForThumbnail, // thumbnail image + others: instances, // all other level instances in the image Pyramid + othersFrameOfReferenceUID, + }; + + return [displaySet]; +} + +export default function getDicomMicroscopySopClassHandler({ + servicesManager, + extensionManager, +}) { + const getDisplaySetsFromSeries = instances => { + return _getDisplaySetsFromSeries( + instances, + servicesManager, + extensionManager + ); + }; + + return { + name: 'DicomMicroscopySopClassHandler', + sopClassUids: [SOP_CLASS_UIDS.VL_WHOLE_SLIDE_MICROSCOPY_IMAGE_STORAGE], + getDisplaySetsFromSeries, + }; +} diff --git a/extensions/dicom-microscopy/src/DicomMicroscopyViewport.css b/extensions/dicom-microscopy/src/DicomMicroscopyViewport.css new file mode 100644 index 000000000..7e10bb501 --- /dev/null +++ b/extensions/dicom-microscopy/src/DicomMicroscopyViewport.css @@ -0,0 +1,352 @@ +.DicomMicroscopyViewer .ol-box { + box-sizing: border-box; + border-radius: 2px; + border: 1.5px solid var(--ol-background-color); + background-color: var(--ol-partial-background-color); +} + +.DicomMicroscopyViewer .ol-mouse-position { + top: 8px; + right: 8px; + position: absolute; +} + +.DicomMicroscopyViewer .ol-scale-line { + background: var(--ol-partial-background-color); + border-radius: 4px; + bottom: 8px; + left: 8px; + padding: 2px; + position: absolute; +} + +.DicomMicroscopyViewer .ol-scale-line-inner { + border: 1px solid var(--ol-subtle-foreground-color); + border-top: none; + color: var(--ol-foreground-color); + font-size: 10px; + text-align: center; + margin: 1px; + will-change: contents, width; + transition: all 0.25s; +} + +.DicomMicroscopyViewer .ol-scale-bar { + position: absolute; + bottom: 8px; + left: 8px; +} + +.DicomMicroscopyViewer .ol-scale-bar-inner { + display: flex; +} + +.DicomMicroscopyViewer .ol-scale-step-marker { + width: 1px; + height: 15px; + background-color: var(--ol-foreground-color); + float: right; + z-index: 10; +} + +.DicomMicroscopyViewer .ol-scale-step-text { + position: absolute; + bottom: -5px; + font-size: 10px; + z-index: 11; + color: var(--ol-foreground-color); + text-shadow: -1.5px 0 var(--ol-partial-background-color), + 0 1.5px var(--ol-partial-background-color), + 1.5px 0 var(--ol-partial-background-color), + 0 -1.5px var(--ol-partial-background-color); +} + +.DicomMicroscopyViewer .ol-scale-text { + position: absolute; + font-size: 12px; + text-align: center; + bottom: 25px; + color: var(--ol-foreground-color); + text-shadow: -1.5px 0 var(--ol-partial-background-color), + 0 1.5px var(--ol-partial-background-color), + 1.5px 0 var(--ol-partial-background-color), + 0 -1.5px var(--ol-partial-background-color); +} + +.DicomMicroscopyViewer .ol-scale-singlebar { + position: relative; + height: 10px; + z-index: 9; + box-sizing: border-box; + border: 1px solid var(--ol-foreground-color); +} + +.DicomMicroscopyViewer .ol-scale-singlebar-even { + background-color: var(--ol-subtle-foreground-color); +} + +.DicomMicroscopyViewer .ol-scale-singlebar-odd { + background-color: var(--ol-background-color); +} + +.DicomMicroscopyViewer .ol-unsupported { + display: none; +} + +.DicomMicroscopyViewer .ol-viewport, +.DicomMicroscopyViewer .ol-unselectable { + -webkit-touch-callout: none; + -webkit-user-select: none; + -moz-user-select: none; + user-select: none; + -webkit-tap-highlight-color: transparent; +} + +.DicomMicroscopyViewer .ol-viewport canvas { + all: unset; +} + +.DicomMicroscopyViewer .ol-selectable { + -webkit-touch-callout: default; + -webkit-user-select: text; + -moz-user-select: text; + user-select: text; +} + +.DicomMicroscopyViewer .ol-grabbing { + cursor: -webkit-grabbing; + cursor: -moz-grabbing; + cursor: grabbing; +} + +.DicomMicroscopyViewer .ol-grab { + cursor: move; + cursor: -webkit-grab; + cursor: -moz-grab; + cursor: grab; +} + +.DicomMicroscopyViewer .ol-control { + position: absolute; + background-color: var(--ol-subtle-background-color); + border-radius: 4px; +} + +.DicomMicroscopyViewer .ol-zoom { + top: 0.5em; + left: 0.5em; +} + +.DicomMicroscopyViewer .ol-rotate { + top: 0.5em; + right: 0.5em; + transition: opacity 0.25s linear, visibility 0s linear; +} + +.DicomMicroscopyViewer .ol-rotate.ol-hidden { + opacity: 0; + visibility: hidden; + transition: opacity 0.25s linear, visibility 0s linear 0.25s; +} + +.DicomMicroscopyViewer .ol-zoom-extent { + top: 4.643em; + left: 0.5em; +} + +.DicomMicroscopyViewer .ol-full-screen { + right: 0.5em; + top: 0.5em; +} + +.DicomMicroscopyViewer .ol-control button { + display: block; + margin: 1px; + padding: 0; + color: var(--ol-subtle-foreground-color); + font-weight: bold; + text-decoration: none; + font-size: inherit; + text-align: center; + height: 1.375em; + width: 1.375em; + line-height: 0.4em; + background-color: var(--ol-background-color); + border: none; + border-radius: 2px; +} + +.DicomMicroscopyViewer .ol-control button::-moz-focus-inner { + border: none; + padding: 0; +} + +.DicomMicroscopyViewer .ol-zoom-extent button { + line-height: 1.4em; +} + +.DicomMicroscopyViewer .ol-compass { + display: block; + font-weight: normal; + will-change: transform; +} + +.DicomMicroscopyViewer .ol-touch .ol-control button { + font-size: 1.5em; +} + +.DicomMicroscopyViewer .ol-touch .ol-zoom-extent { + top: 5.5em; +} + +.DicomMicroscopyViewer .ol-control button:hover, +.DicomMicroscopyViewer .ol-control button:focus { + text-decoration: none; + outline: 1px solid var(--ol-subtle-foreground-color); + color: var(--ol-foreground-color); +} + +.DicomMicroscopyViewer .ol-zoom .ol-zoom-in { + border-radius: 2px 2px 0 0; +} + +.DicomMicroscopyViewer .ol-zoom .ol-zoom-out { + border-radius: 0 0 2px 2px; +} + +.DicomMicroscopyViewer .ol-attribution { + text-align: right; + bottom: 0.5em; + right: 0.5em; + max-width: calc(100% - 1.3em); + display: flex; + flex-flow: row-reverse; + align-items: center; +} + +.DicomMicroscopyViewer .ol-attribution a { + color: var(--ol-subtle-foreground-color); + text-decoration: none; +} + +.DicomMicroscopyViewer .ol-attribution ul { + margin: 0; + padding: 1px 0.5em; + color: var(--ol-foreground-color); + text-shadow: 0 0 2px var(--ol-background-color); + font-size: 12px; +} + +.DicomMicroscopyViewer .ol-attribution li { + display: inline; + list-style: none; +} + +.DicomMicroscopyViewer .ol-attribution li:not(:last-child):after { + content: ' '; +} + +.DicomMicroscopyViewer .ol-attribution img { + max-height: 2em; + max-width: inherit; + vertical-align: middle; +} + +.DicomMicroscopyViewer .ol-attribution button { + flex-shrink: 0; +} + +.DicomMicroscopyViewer .ol-attribution.ol-collapsed ul { + display: none; +} + +.DicomMicroscopyViewer .ol-attribution:not(.ol-collapsed) { + background: var(--ol-partial-background-color); +} + +.DicomMicroscopyViewer .ol-attribution.ol-uncollapsible { + bottom: 0; + right: 0; + border-radius: 4px 0 0; +} + +.DicomMicroscopyViewer .ol-attribution.ol-uncollapsible img { + margin-top: -0.2em; + max-height: 1.6em; +} + +.DicomMicroscopyViewer .ol-attribution.ol-uncollapsible button { + display: none; +} + +.DicomMicroscopyViewer .ol-zoomslider { + top: 4.5em; + left: 0.5em; + height: 200px; +} + +.DicomMicroscopyViewer .ol-zoomslider button { + position: relative; + height: 10px; +} + +.DicomMicroscopyViewer .ol-touch .ol-zoomslider { + top: 5.5em; +} + +.DicomMicroscopyViewer .ol-overviewmap { + left: 0.5em; + bottom: 0.5em; +} + +.DicomMicroscopyViewer .ol-overviewmap.ol-uncollapsible { + bottom: 0; + left: 0; + border-radius: 0 4px 0 0; +} + +.DicomMicroscopyViewer .ol-overviewmap .ol-overviewmap-map, +.DicomMicroscopyViewer .ol-overviewmap button { + display: block; +} + +.DicomMicroscopyViewer .ol-overviewmap .ol-overviewmap-map { + border: 1px solid var(--ol-subtle-foreground-color); + height: 150px; + width: 150px; +} + +.DicomMicroscopyViewer .ol-overviewmap:not(.ol-collapsed) button { + bottom: 0; + left: 0; + position: absolute; +} + +.DicomMicroscopyViewer .ol-overviewmap.ol-collapsed .ol-overviewmap-map, +.DicomMicroscopyViewer .ol-overviewmap.ol-uncollapsible button { + display: none; +} + +.DicomMicroscopyViewer .ol-overviewmap:not(.ol-collapsed) { + background: var(--ol-subtle-background-color); +} + +.DicomMicroscopyViewer .ol-overviewmap-box { + border: 1.5px dotted var(--ol-subtle-foreground-color); +} + +.DicomMicroscopyViewer .ol-overviewmap .ol-overviewmap-box:hover { + cursor: move; +} + +@layout-header-background: #007ea3; +@primary-color: #007ea3; +@processing-color: #8cb8c6; +@success-color: #3f9c35; +@warning-color: #eeaf30; +@error-color: #96172e; +@font-size-base: 14px; + +.DicomMicroscopyViewer .ol-tooltip { + font-size: 16px !important; +} diff --git a/extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx b/extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx new file mode 100644 index 000000000..329760604 --- /dev/null +++ b/extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx @@ -0,0 +1,321 @@ +import React, { Component } from 'react'; +import ReactResizeDetector from 'react-resize-detector'; +import PropTypes from 'prop-types'; +import debounce from 'lodash.debounce'; + +import './DicomMicroscopyViewport.css'; +import ViewportOverlay from './components/ViewportOverlay'; +import getDicomWebClient from './utils/dicomWebClient'; +import dcmjs from 'dcmjs'; +import cleanDenaturalizedDataset from './utils/cleanDenaturalizedDataset'; +import MicroscopyService from './services/MicroscopyService'; + +class DicomMicroscopyViewport extends Component { + state = { + error: null as any, + }; + + microscopyService: MicroscopyService; + viewer: any = null; // dicom-microscopy-viewer instance + managedViewer: any = null; // managed wrapper of microscopy-dicom extension + + container = React.createRef(); + overlayElement = React.createRef(); + debouncedResize: () => any; + + constructor(props: any) { + super(props); + + const { microscopyService } = this.props.servicesManager.services; + this.microscopyService = microscopyService; + this.debouncedResize = debounce(() => { + if (this.viewer) this.viewer.resize(); + }, 100); + } + + static propTypes = { + viewportData: PropTypes.object, + activeViewportIndex: PropTypes.number, + setViewportActive: PropTypes.func, + + // props from OHIF Viewport Grid + displaySets: PropTypes.array, + viewportIndex: PropTypes.number, + viewportLabel: PropTypes.string, + dataSource: PropTypes.object, + viewportOptions: PropTypes.object, + displaySetOptions: PropTypes.array, + + // other props from wrapping component + servicesManager: PropTypes.object, + extensionManager: PropTypes.object, + commandsManager: PropTypes.object, + }; + + /** + * Get the nearest ROI from the mouse click point + * + * @param event + * @param autoselect + * @returns + */ + getNearbyROI(event: Event, autoselect = true) { + const symbols = Object.getOwnPropertySymbols(this.viewer); + const _drawingSource = symbols.find(p => p.description === 'drawingSource'); + const _pyramid = symbols.find(p => p.description === 'pyramid'); + const _map = symbols.find(p => p.description === 'map'); + const _affine = symbols.find(p => p.description === 'affine'); + + const feature = this.viewer[_drawingSource].getClosestFeatureToCoordinate( + this.viewer[_map].getEventCoordinate(event) + ); + + if (!feature) { + return null; + } + + const roiAnnotation = this.viewer._getROIFromFeature( + feature, + this.viewer[_pyramid].metadata, + this.viewer[_affine] + ); + if (roiAnnotation && autoselect) { + this.microscopyService.selectAnnotation(roiAnnotation); + } + return roiAnnotation; + } + + // install the microscopy renderer into the web page. + // you should only do this once. + async installOpenLayersRenderer(container, displaySet) { + const loadViewer = async metadata => { + const { + viewer: DicomMicroscopyViewer, + metadata: metadataUtils, + } = await import( + /* webpackChunkName: "dicom-microscopy-viewer" */ 'dicom-microscopy-viewer' + ); + const microscopyViewer = DicomMicroscopyViewer.VolumeImageViewer; + + const client = getDicomWebClient({ + extensionManager: this.props.extensionManager, + servicesManager: this.props.servicesManager, + }); + + // Parse, format, and filter metadata + const volumeImages: any[] = []; + + /** + * This block of code is the original way of loading DICOM into dicom-microscopy-viewer + * as in their documentation. + * But we have the metadata already loaded by our loaders. + * As the metadata for microscopy DIOM files tends to be big and we don't + * want to double load it, below we have the mechanism to reconstruct the + * DICOM JSON structure (denaturalized) from naturalized metadata. + * (NOTE: Our loaders cache only naturalized metadata, not the denaturalized.) + */ + // { + // const retrieveOptions = { + // studyInstanceUID: metadata[0].StudyInstanceUID, + // seriesInstanceUID: metadata[0].SeriesInstanceUID, + // }; + // metadata = await client.retrieveSeriesMetadata(retrieveOptions); + // // Parse, format, and filter metadata + // metadata.forEach(m => { + // if ( + // volumeImages.length > 0 && + // m['00200052'].Value[0] != volumeImages[0].FrameOfReferenceUID + // ) { + // console.warn( + // 'Expected FrameOfReferenceUID of difference instances within a series to be the same, found multiple different values', + // m['00200052'].Value[0] + // ); + // m['00200052'].Value[0] = volumeImages[0].FrameOfReferenceUID; + // } + // const image = new metadataUtils.VLWholeSlideMicroscopyImage({ + // metadata: m, + // }); + // const imageFlavor = image.ImageType[2]; + // if (imageFlavor === 'VOLUME' || imageFlavor === 'THUMBNAIL') { + // volumeImages.push(image); + // } + // }); + // } + + metadata.forEach(m => { + const inst = cleanDenaturalizedDataset( + dcmjs.data.DicomMetaDictionary.denaturalizeDataset(m) + ); + if (!inst['00480105']) { + // Optical Path Sequence, no OpticalPathIdentifier? + // NOTE: this is actually a not-well formatted DICOM VL Whole Slide Microscopy Image. + inst['00480105'] = { + vr: 'SQ', + Value: [ + { + '00480106': { + vr: 'SH', + Value: ['1'], + }, + }, + ], + }; + } + const image = new metadataUtils.VLWholeSlideMicroscopyImage({ + metadata: inst, + }); + const imageFlavor = image.ImageType[2]; + if (imageFlavor === 'VOLUME' || imageFlavor === 'THUMBNAIL') { + volumeImages.push(image); + } + }); + + // format metadata for microscopy-viewer + const options = { + client, + metadata: volumeImages, + retrieveRendered: false, + controls: ['overview', 'position', 'zoom'], + }; + + this.viewer = new microscopyViewer(options); + + if ( + this.overlayElement && + this.overlayElement.current && + this.viewer.addViewportOverlay + ) { + this.viewer.addViewportOverlay({ + element: this.overlayElement.current, + coordinates: [0, 0], // TODO: dicom-microscopy-viewer documentation says this can be false to be automatically, but it is not. + navigate: true, + className: 'OpenLayersOverlay', + }); + } + + this.viewer.render({ container }); + + const { StudyInstanceUID, SeriesInstanceUID } = displaySet; + + this.managedViewer = this.microscopyService.addViewer( + this.viewer, + this.props.viewportIndex, + container, + StudyInstanceUID, + SeriesInstanceUID + ); + + this.managedViewer.addContextMenuCallback((event: Event) => { + // TODO: refactor this after Bill's changes on ContextMenu feature get merged + // const roiAnnotationNearBy = this.getNearbyROI(event); + }); + }; + + this.microscopyService.clearAnnotations(); + + let smDisplaySet = displaySet; + if (displaySet.Modality === 'SR') { + // for SR displaySet, let's load the actual image displaySet + smDisplaySet = displaySet.getSourceDisplaySet(); + } + console.log('Loading viewer metadata', smDisplaySet); + + await loadViewer(smDisplaySet.others); + + if (displaySet.Modality === 'SR') { + displaySet.load(smDisplaySet); + } + } + + componentDidMount() { + const { displaySets, viewportIndex } = this.props; + const displaySet = displaySets[viewportIndex]; + this.installOpenLayersRenderer(this.container.current, displaySet); + } + + componentDidUpdate( + prevProps: Readonly<{}>, + prevState: Readonly<{}>, + snapshot?: any + ): void { + if ( + this.managedViewer && + prevProps.displaySets !== this.props.displaySets + ) { + const { displaySets } = this.props; + const displaySet = displaySets[0]; + + this.microscopyService.clearAnnotations(); + + // loading SR + if (displaySet.Modality === 'SR') { + const referencedDisplaySet = displaySet.getSourceDisplaySet(); + displaySet.load(referencedDisplaySet); + } + } + } + + componentWillUnmount() { + this.microscopyService.removeViewer(this.viewer); + } + + setViewportActiveHandler = () => { + const { + setViewportActive, + viewportIndex, + activeViewportIndex, + } = this.props; + + if (viewportIndex !== activeViewportIndex) { + setViewportActive(viewportIndex); + } + }; + + render() { + const style = { width: '100%', height: '100%' }; + const displaySet = this.props.displaySets[0]; + const firstInstance = displaySet.firstInstance || displaySet.instance; + + return ( +
+
+
+
+ {displaySet && firstInstance.imageId && ( + + )} +
+
+
+ {ReactResizeDetector && ( + + )} + {this.state.error ? ( +

{JSON.stringify(this.state.error)}

+ ) : ( +
+ )} +
+ ); + } + + onWindowResize = () => { + this.debouncedResize(); + }; +} + +export default DicomMicroscopyViewport; diff --git a/extensions/dicom-microscopy/src/components/MicroscopyPanel/MicroscopyPanel.tsx b/extensions/dicom-microscopy/src/components/MicroscopyPanel/MicroscopyPanel.tsx new file mode 100644 index 000000000..88d5f4392 --- /dev/null +++ b/extensions/dicom-microscopy/src/components/MicroscopyPanel/MicroscopyPanel.tsx @@ -0,0 +1,413 @@ +import React, { useState, useEffect } from 'react'; +import PropTypes from 'prop-types'; +import { + ServicesManager, + ExtensionManager, + CommandsManager, + DicomMetadataStore, +} from '@ohif/core'; +import { MeasurementTable, Icon, ButtonGroup, Button } from '@ohif/ui'; +import { withTranslation, WithTranslation } from 'react-i18next'; +import { EVENTS as MicroscopyEvents } from '../../services/MicroscopyService'; +import dcmjs from 'dcmjs'; +import styles from '../../utils/styles'; +import callInputDialog from '../../utils/callInputDialog'; +import constructSR from '../../utils/constructSR'; +import { saveByteArray } from '../../utils/saveByteArray'; + +let saving = false; +const { datasetToBuffer } = dcmjs.data; + +const formatArea = area => { + let mult = 1; + let unit = 'mm'; + if (area > 1000000) { + unit = 'm'; + mult = 1 / 1000000; + } else if (area < 1) { + unit = 'μm'; + mult = 1000000; + } + return `${(area * mult).toFixed(2)} ${unit}²`; +}; + +const formatLength = (length, unit) => { + let mult = 1; + if (unit == 'km' || (!unit && length > 1000000)) { + unit = 'km'; + mult = 1 / 1000000; + } else if (unit == 'm' || (!unit && length > 1000)) { + unit = 'm'; + mult = 1 / 1000; + } else if (unit == 'μm' || (!unit && length < 1)) { + unit = 'μm'; + mult = 1000; + } else if (unit && unit != 'mm') { + throw new Error(`Unknown length unit ${unit}`); + } else { + unit = 'mm'; + } + return `${(length * mult).toFixed(2)} ${unit}`; +}; + +interface IMicroscopyPanelProps extends WithTranslation { + viewports: PropTypes.array; + activeViewportIndex: PropTypes.number; + + // + onSaveComplete?: PropTypes.func; // callback when successfully saved annotations + onRejectComplete?: PropTypes.func; // callback when rejected annotations + + // + servicesManager: ServicesManager; + extensionManager: ExtensionManager; + commandsManager: CommandsManager; +} + +/** + * Microscopy Measurements Panel Component + * + * @param props + * @returns + */ +function MicroscopyPanel(props: IMicroscopyPanelProps) { + const { microscopyService } = props.servicesManager.services; + + const [studyInstanceUID, setStudyInstanceUID] = useState( + null as string | null + ); + const [roiAnnotations, setRoiAnnotations] = useState([] as any[]); + const [selectedAnnotation, setSelectedAnnotation] = useState(null as any); + const { servicesManager, extensionManager } = props; + + const { uiDialogService, displaySetService } = servicesManager.services; + + useEffect(() => { + const viewport = props.viewports[props.activeViewportIndex]; + if (viewport.displaySetInstanceUIDs[0]) { + const displaySet = displaySetService.getDisplaySetByUID( + viewport.displaySetInstanceUIDs[0] + ); + if (displaySet) { + setStudyInstanceUID(displaySet.StudyInstanceUID); + } + } + }, [props.viewports, props.activeViewportIndex]); + + useEffect(() => { + const onAnnotationUpdated = () => { + const roiAnnotations = microscopyService.getAnnotationsForStudy( + studyInstanceUID + ); + setRoiAnnotations(roiAnnotations); + }; + + const onAnnotationSelected = () => { + const selectedAnnotation = microscopyService.getSelectedAnnotation(); + setSelectedAnnotation(selectedAnnotation); + }; + + const onAnnotationRemoved = () => { + onAnnotationUpdated(); + }; + + const { + unsubscribe: unsubscribeAnnotationUpdated, + } = microscopyService.subscribe( + MicroscopyEvents.ANNOTATION_UPDATED, + onAnnotationUpdated + ); + const { + unsubscribe: unsubscribeAnnotationSelected, + } = microscopyService.subscribe( + MicroscopyEvents.ANNOTATION_SELECTED, + onAnnotationSelected + ); + const { + unsubscribe: unsubscribeAnnotationRemoved, + } = microscopyService.subscribe( + MicroscopyEvents.ANNOTATION_REMOVED, + onAnnotationRemoved + ); + onAnnotationUpdated(); + onAnnotationSelected(); + + // on unload unsubscribe from events + return () => { + unsubscribeAnnotationUpdated(); + unsubscribeAnnotationSelected(); + unsubscribeAnnotationRemoved(); + }; + }, [studyInstanceUID]); + + /** + * On clicking "Save Annotations" button, prompt an input modal for the + * new series' description, and continue to save. + * + * @returns + */ + const promptSave = () => { + const annotations = microscopyService.getAnnotationsForStudy( + studyInstanceUID + ); + + if (!annotations || saving) { + return; + } + + callInputDialog({ + uiDialogService, + title: 'Enter description of the Series', + defaultValue: '', + callback: (value: string, action: string) => { + switch (action) { + case 'save': { + saveFunction(value); + } + } + }, + }); + }; + + const getAllDisplaySets = (studyMetadata: any) => { + let allDisplaySets = [] as any[]; + studyMetadata.series.forEach((series: any) => { + const displaySets = displaySetService.getDisplaySetsForSeries( + series.SeriesInstanceUID + ); + allDisplaySets = allDisplaySets.concat(displaySets); + }); + return allDisplaySets; + }; + + /** + * Save annotations as a series + * + * @param SeriesDescription - series description + * @returns + */ + const saveFunction = async (SeriesDescription: string) => { + const dataSource = extensionManager.getActiveDataSource()[0]; + const { onSaveComplete } = props; + const annotations = microscopyService.getAnnotationsForStudy( + studyInstanceUID + ); + + saving = true; + + // There is only one viewer possible for one study, + // Since once study contains multiple resolution levels (series) of one whole + // Slide image. + + const studyMetadata = DicomMetadataStore.getStudy(studyInstanceUID); + const displaySets = getAllDisplaySets(studyMetadata); + const smDisplaySet = displaySets.find(ds => ds.Modality === 'SM'); + + // Get the next available series number after 4700. + + const dsWithMetadata = displaySets.filter( + ds => + ds.metadata && + ds.metadata.SeriesNumber && + typeof ds.metadata.SeriesNumber === 'number' + ); + + // Generate next series number + const seriesNumbers = dsWithMetadata.map(ds => ds.metadata.SeriesNumber); + const maxSeriesNumber = Math.max(...seriesNumbers, 4700); + const SeriesNumber = maxSeriesNumber + 1; + + const { instance: metadata } = smDisplaySet; + + // construct SR dataset + const dataset = constructSR( + metadata, + { SeriesDescription, SeriesNumber }, + annotations + ); + + // Save in DICOM format + try { + if (dataSource) { + if (dataSource.wadoRoot == 'saveDicom') { + // download as DICOM file + const part10Buffer = datasetToBuffer(dataset); + saveByteArray(part10Buffer, `sr-microscopy.dcm`); + } else { + // Save into Web Data source + const { StudyInstanceUID } = dataset; + await dataSource.store.dicom(dataset); + if (StudyInstanceUID) { + dataSource.deleteStudyMetadataPromise(StudyInstanceUID); + } + } + onSaveComplete({ + title: 'SR Saved', + meassage: 'Measurements downloaded successfully', + type: 'success', + }); + } else { + console.error('Server unspecified'); + } + } catch (error) { + onSaveComplete({ + title: 'SR Save Failed', + message: error.message || error.toString(), + type: 'error', + }); + } finally { + saving = false; + } + }; + + /** + * On clicking "Reject annotations" button + */ + const onDeleteCurrentSRHandler = async () => { + try { + const activeViewport = props.viewports[props.activeViewportIndex]; + const { StudyInstanceUID } = activeViewport; + + // TODO: studies? + const study = DicomMetadataStore.getStudy(StudyInstanceUID); + + const lastDerivedDisplaySet = study.derivedDisplaySets.sort( + (ds1: any, ds2: any) => { + const dateTime1 = Number(`${ds1.SeriesDate}${ds1.SeriesTime}`); + const dateTime2 = Number(`${ds2.SeriesDate}${ds2.SeriesTime}`); + return dateTime1 > dateTime2; + } + )[study.derivedDisplaySets.length - 1]; + + // TODO: use dataSource.reject.dicom() + // await DICOMSR.rejectMeasurements( + // study.wadoRoot, + // lastDerivedDisplaySet.StudyInstanceUID, + // lastDerivedDisplaySet.SeriesInstanceUID + // ); + props.onRejectComplete({ + title: 'Report rejected', + message: 'Latest report rejected successfully', + type: 'success', + }); + } catch (error) { + props.onRejectComplete({ + title: 'Failed to reject report', + message: error.message, + type: 'error', + }); + } + }; + + /** + * Handler for clicking event of an annotation item. + * + * @param param0 + */ + const onMeasurementItemClickHandler = ({ uid }: { uid: string }) => { + const roiAnnotation = microscopyService.getAnnotation(uid); + microscopyService.selectAnnotation(roiAnnotation); + microscopyService.focusAnnotation(roiAnnotation, props.activeViewportIndex); + }; + + /** + * Handler for "Edit" action of an annotation item + * @param param0 + */ + const onMeasurementItemEditHandler = ({ + uid, + isActive, + }: { + uid: string; + isActive: boolean; + }) => { + props.commandsManager.runCommand('setLabel', { uid }, 'MICROSCOPY'); + }; + + // Convert ROI annotations managed by microscopyService into our + // own format for display + const data = roiAnnotations.map((roiAnnotation, index) => { + const label = roiAnnotation.getDetailedLabel(); + const area = roiAnnotation.getArea(); + const length = roiAnnotation.getLength(); + const shortAxisLength = roiAnnotation.roiGraphic.properties.shortAxisLength; + const isSelected: boolean = selectedAnnotation === roiAnnotation; + + // other events + const { uid } = roiAnnotation; + + // display text + const displayText = []; + + if (area !== undefined) { + displayText.push(formatArea(area)); + } else if (length !== undefined) { + displayText.push( + shortAxisLength + ? `${formatLength(length, 'μm')} x ${formatLength( + shortAxisLength, + 'μm' + )}` + : `${formatLength(length, 'μm')}` + ); + } + + // convert to measurementItem format compatible with component + return { + uid, + index, + label, + isActive: isSelected, + displayText, + roiAnnotation, + }; + }); + + const disabled = data.length === 0; + + return ( + <> +
+ +
+
+ + {/* Let's hide the save button for now, as export SR for SM is a proof of concept */} + {/*{promptSave && ( + + )} */} + {/* */} + +
+ + ); +} + +const connectedMicroscopyPanel = withTranslation(['MicroscopyTable', 'Common'])( + MicroscopyPanel +); + +export default connectedMicroscopyPanel; diff --git a/extensions/dicom-microscopy/src/components/ViewportOverlay/ViewportOverlay.css b/extensions/dicom-microscopy/src/components/ViewportOverlay/ViewportOverlay.css new file mode 100644 index 000000000..da46120c5 --- /dev/null +++ b/extensions/dicom-microscopy/src/components/ViewportOverlay/ViewportOverlay.css @@ -0,0 +1,87 @@ +.DicomMicroscopyViewer .OpenLayersOverlay { + height: 100%; + width: 100%; + display: block !important; + pointer-events: none !important; +} + +.DicomMicroscopyViewer .text-primary-light { + font-size: 14px; + color: yellow; + font-weight: normal; +} + +.DicomMicroscopyViewer .text-primary-light span { + overflow: hidden; + white-space: nowrap; + text-overflow: ellipsis; + max-width: 300px; + /* text-shadow: 0px 1px 1px rgba(225, 225, 225, 0.6), + 0px 1px 1px rgba(225, 225, 225, 0.6), + 1px 1px 3px rgba(225, 225, 225, 0.9), + 1px 1px 3px rgba(225, 225, 225, 0.9), + 1px 1px 3px rgba(225, 225, 225, 0.9), + 1px 1px 3px rgba(225, 225, 225, 0.9); */ +} + +.DicomMicroscopyViewer .absolute { + position: absolute; +} + +.DicomMicroscopyViewer .flex { + display: flex; +} + +.DicomMicroscopyViewer .flex-row { + flex-direction: row; +} + +.DicomMicroscopyViewer .flex-col { + flex-direction: column; +} + +.DicomMicroscopyViewer .pointer-events-none { + pointer-events: none; +} + +.DicomMicroscopyViewer .left-viewport-scrollbar { + left: 0.5rem; +} + +.DicomMicroscopyViewer .right-viewport-scrollbar { + right: 1.3rem; +} + +.DicomMicroscopyViewer .top-viewport { + top: 0.5rem; +} + +.DicomMicroscopyViewer .bottom-viewport { + bottom: 0.5rem; +} + +.DicomMicroscopyViewer .bottom-viewport.left-viewport { + bottom: 0.5rem; + left: calc(0.5rem + 250px); +} + +.DicomMicroscopyViewer .right-viewport-scrollbar .flex { + justify-content: end; +} + +.DicomMicroscopyViewer .microscopy-viewport-overlay { + padding: 0.5rem 1rem; + background: rgba(0, 0, 0, 0.5); + max-width: 40%; +} + +.DicomMicroscopyViewer .microscopy-viewport-overlay .flex { + max-width: 100%; + overflow: hidden; + text-overflow: ellipsis; + white-space: nowrap; +} + +.DicomMicroscopyViewer .top-viewport .flex span:not(.font-light) { + flex-shrink: 0; +} \ No newline at end of file diff --git a/extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx b/extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx new file mode 100644 index 000000000..bbe863e71 --- /dev/null +++ b/extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx @@ -0,0 +1,155 @@ +import React from 'react'; +import classnames from 'classnames'; +import ConfigPoint from 'config-point'; + +import listComponentGenerator from './listComponentGenerator'; +import './ViewportOverlay.css'; +import { + formatDICOMDate, + formatDICOMTime, + formatNumberPrecision, + formatPN, +} from './utils'; + +interface OverylayItem { + id: string; + title: string; + value?: (props: any) => string; + condition?: (props: any) => boolean; + contents?: (props: any) => { className: string; value: any }; + generator?: (props: any) => any; +} + +/** + * + * @param {*} config is a configuration object that defines four lists of elements, + * one topLeft, topRight, bottomLeft, bottomRight contents. + * @param {*} extensionManager is used to load the image data. + * @returns + */ +export const generateFromConfig = ({ + topLeft, + topRight, + bottomLeft, + bottomRight, + itemGenerator, +}: { + topLeft: OverylayItem[]; + topRight: OverylayItem[]; + bottomLeft: OverylayItem[]; + bottomRight: OverylayItem[]; + itemGenerator: (props: any) => any; +}) => { + return (props: any) => { + const topLeftClass = 'top-viewport left-viewport text-primary-light'; + const topRightClass = + 'top-viewport right-viewport-scrollbar text-primary-light'; + const bottomRightClass = + 'bottom-viewport right-viewport-scrollbar text-primary-light'; + const bottomLeftClass = 'bottom-viewport left-viewport text-primary-light'; + const overlay = 'absolute pointer-events-none microscopy-viewport-overlay'; + + return ( + <> + {topLeft && topLeft.length > 0 && ( +
+ {listComponentGenerator({ ...props, list: topLeft, itemGenerator })} +
+ )} + {topRight && topRight.length > 0 && ( +
+ {listComponentGenerator({ + ...props, + list: topRight, + itemGenerator, + })} +
+ )} + {bottomRight && bottomRight.length > 0 && ( +
+ {listComponentGenerator({ + ...props, + list: bottomRight, + itemGenerator, + })} +
+ )} + {bottomLeft && bottomLeft.length > 0 && ( +
+ {listComponentGenerator({ + ...props, + list: bottomLeft, + itemGenerator, + })} +
+ )} + + ); + }; +}; + +const itemGenerator = (props: any) => { + const { item } = props; + const { title, value: valueFunc, condition, contents } = item; + props.image = { ...props.image, ...props.metadata }; + props.formatDate = formatDICOMDate; + props.formatTime = formatDICOMTime; + props.formatPN = formatPN; + props.formatNumberPrecision = formatNumberPrecision; + if (condition && !condition(props)) return null; + if (!contents && !valueFunc) return null; + const value = valueFunc && valueFunc(props); + const contentsValue = (contents && contents(props)) || [ + { className: 'mr-1', value: title }, + { classname: 'mr-1 font-light', value }, + ]; + + return ( +
+ {contentsValue.map((content, idx) => ( + + {content.value} + + ))} +
+ ); +}; + +const { MicroscopyViewportOverlay } = ConfigPoint.register({ + MicroscopyViewportOverlay: { + configBase: { + topLeft: [ + // { + // id: 'sm-overlay-patient-name', + // title: 'PatientName', + // condition: ({ instance }) => + // instance && instance.PatientName && instance.PatientName.Alphabetic, + // value: ({ instance }) => + // instance.PatientName && instance.PatientName.Alphabetic, + // } as OverylayItem, + ], + topRight: [] as OverylayItem[], + bottomLeft: [] as OverylayItem[], + bottomRight: [] as OverylayItem[], + itemGenerator, + generateFromConfig, + }, + ...(window.config?.MicroscopyViewportOverlay || {}), + }, +}); + +export default MicroscopyViewportOverlay.generateFromConfig( + MicroscopyViewportOverlay +); diff --git a/extensions/dicom-microscopy/src/components/ViewportOverlay/listComponentGenerator.tsx b/extensions/dicom-microscopy/src/components/ViewportOverlay/listComponentGenerator.tsx new file mode 100644 index 000000000..04150625d --- /dev/null +++ b/extensions/dicom-microscopy/src/components/ViewportOverlay/listComponentGenerator.tsx @@ -0,0 +1,12 @@ +const listComponentGenerator = props => { + const { list, itemGenerator } = props; + if (!list) return; + return list.map(item => { + if (!item) return; + const generator = item.generator || itemGenerator; + if (!generator) throw new Error(`No generator for ${item}`); + return generator({ ...props, item }); + }); +}; + +export default listComponentGenerator; diff --git a/extensions/dicom-microscopy/src/components/ViewportOverlay/utils.ts b/extensions/dicom-microscopy/src/components/ViewportOverlay/utils.ts new file mode 100644 index 000000000..81f56ad05 --- /dev/null +++ b/extensions/dicom-microscopy/src/components/ViewportOverlay/utils.ts @@ -0,0 +1,102 @@ +import moment from 'moment'; +import * as cornerstone from '@cornerstonejs/core'; + +/** + * Checks if value is valid. + * + * @param {number} value + * @returns {boolean} is valid. + */ +export function isValidNumber(value) { + return typeof value === 'number' && !isNaN(value); +} + +/** + * Formats number precision. + * + * @param {number} number + * @param {number} precision + * @returns {number} formatted number. + */ +export function formatNumberPrecision(number, precision) { + if (number !== null) { + return parseFloat(number).toFixed(precision); + } +} + +/** + * Formats DICOM date. + * + * @param {string} date + * @param {string} strFormat + * @returns {string} formatted date. + */ +export function formatDICOMDate(date, strFormat = 'MMM D, YYYY') { + return moment(date, 'YYYYMMDD').format(strFormat); +} + +/** + * DICOM Time is stored as HHmmss.SSS, where: + * HH 24 hour time: + * m mm 0..59 Minutes + * s ss 0..59 Seconds + * S SS SSS 0..999 Fractional seconds + * + * Goal: '24:12:12' + * + * @param {*} time + * @param {string} strFormat + * @returns {string} formatted name. + */ +export function formatDICOMTime(time, strFormat = 'HH:mm:ss') { + return moment(time, 'HH:mm:ss').format(strFormat); +} + +/** + * Formats a patient name for display purposes + * + * @param {string} name + * @returns {string} formatted name. + */ +export function formatPN(name) { + if (!name) { + return; + } + + // Convert the first ^ to a ', '. String.replace() only affects + // the first appearance of the character. + const commaBetweenFirstAndLast = name.replace('^', ', '); + + // Replace any remaining '^' characters with spaces + const cleaned = commaBetweenFirstAndLast.replace(/\^/g, ' '); + + // Trim any extraneous whitespace + return cleaned.trim(); +} + +/** + * Gets compression type + * + * @param {number} imageId + * @returns {string} comrpession type. + */ +export function getCompression(imageId) { + const generalImageModule = + cornerstone.metaData.get('generalImageModule', imageId) || {}; + const { + lossyImageCompression, + lossyImageCompressionRatio, + lossyImageCompressionMethod, + } = generalImageModule; + + if (lossyImageCompression === '01' && lossyImageCompressionRatio !== '') { + const compressionMethod = lossyImageCompressionMethod || 'Lossy: '; + const compressionRatio = formatNumberPrecision( + lossyImageCompressionRatio, + 2 + ); + return compressionMethod + compressionRatio + ' : 1'; + } + + return 'Lossless / Uncompressed'; +} diff --git a/extensions/dicom-microscopy/src/getCommandsModule.ts b/extensions/dicom-microscopy/src/getCommandsModule.ts new file mode 100644 index 000000000..db8210623 --- /dev/null +++ b/extensions/dicom-microscopy/src/getCommandsModule.ts @@ -0,0 +1,198 @@ +import { ServicesManager, CommandsManager, ExtensionManager } from '@ohif/core'; +import styles from './utils/styles'; +import callInputDialog from './utils/callInputDialog'; + +export default function getCommandsModule({ + servicesManager, + commandsManager, + extensionManager, +}: { + servicesManager: ServicesManager; + commandsManager: CommandsManager; + extensionManager: ExtensionManager; +}) { + const { + viewportGridService, + uiDialogService, + microscopyService, + } = servicesManager.services; + + const actions = { + // Measurement tool commands: + deleteMeasurement: ({ uid }) => { + if (uid) { + const roiAnnotation = microscopyService.getAnnotation(uid); + if (roiAnnotation) microscopyService.removeAnnotation(roiAnnotation); + } + }, + + setLabel: ({ uid }) => { + const roiAnnotation = microscopyService.getAnnotation(uid); + + callInputDialog({ + uiDialogService, + title: 'Enter your annotation', + defaultValue: '', + callback: (value: string, action: string) => { + switch (action) { + case 'save': { + roiAnnotation.setLabel(value); + microscopyService.triggerRelabel(roiAnnotation); + } + } + }, + }); + }, + + setToolActive: ({ toolName, toolGroupId = 'MICROSCOPY' }) => { + const dragPanOnMiddle = [ + 'dragPan', + { + bindings: { + mouseButtons: ['middle'], + }, + }, + ]; + const dragZoomOnRight = [ + 'dragZoom', + { + bindings: { + mouseButtons: ['right'], + }, + }, + ]; + if ( + [ + 'line', + 'box', + 'circle', + 'point', + 'polygon', + 'freehandpolygon', + 'freehandline', + ].indexOf(toolName) >= 0 + ) { + // TODO: read from configuration + let options = { + geometryType: toolName, + vertexEnabled: true, + styleOptions: styles.default, + bindings: { + mouseButtons: ['left'], + }, + } as any; + if ('line' === toolName) { + options.minPoints = 2; + options.maxPoints = 2; + } else if ('point' === toolName) { + delete options.styleOptions; + delete options.vertexEnabled; + } + + microscopyService.activateInteractions([ + ['draw', options], + dragPanOnMiddle, + dragZoomOnRight, + ]); + } else if (toolName == 'dragPan') { + microscopyService.activateInteractions([ + [ + 'dragPan', + { + bindings: { + mouseButtons: ['left', 'middle'], + }, + }, + ], + dragZoomOnRight, + ]); + } else { + microscopyService.activateInteractions([ + [ + toolName, + { + bindings: { + mouseButtons: ['left'], + }, + }, + ], + dragPanOnMiddle, + dragZoomOnRight, + ]); + } + }, + + incrementActiveViewport: () => { + const { activeViewportIndex, viewports } = viewportGridService.getState(); + const nextViewportIndex = (activeViewportIndex + 1) % viewports.length; + viewportGridService.setActiveViewportIndex(nextViewportIndex); + }, + decrementActiveViewport: () => { + const { activeViewportIndex, viewports } = viewportGridService.getState(); + const nextViewportIndex = + (activeViewportIndex - 1 + viewports.length) % viewports.length; + viewportGridService.setActiveViewportIndex(nextViewportIndex); + }, + + toggleOverlays: () => { + // overlay + const overlays = document.getElementsByClassName( + 'microscopy-viewport-overlay' + ); + let onoff = false; // true if this will toggle on + for (let i = 0; i < overlays.length; i++) { + if (i === 0) onoff = overlays.item(0).classList.contains('hidden'); + overlays.item(i).classList.toggle('hidden'); + } + + // overview + const { activeViewportIndex, viewports } = viewportGridService.getState(); + microscopyService.toggleOverviewMap(activeViewportIndex); + }, + toggleAnnotations: () => { + microscopyService.toggleROIsVisibility(); + }, + }; + + const definitions = { + deleteMeasurement: { + commandFn: actions.deleteMeasurement, + storeContexts: [] as any[], + options: {}, + }, + setLabel: { + commandFn: actions.setLabel, + storeContexts: [] as any[], + options: {}, + }, + setToolActive: { + commandFn: actions.setToolActive, + storeContexts: [] as any[], + options: {}, + }, + incrementActiveViewport: { + commandFn: actions.incrementActiveViewport, + storeContexts: [] as any[], + }, + decrementActiveViewport: { + commandFn: actions.decrementActiveViewport, + storeContexts: [] as any[], + }, + toggleOverlays: { + commandFn: actions.toggleOverlays, + storeContexts: [] as any[], + options: {}, + }, + toggleAnnotations: { + commandFn: actions.toggleAnnotations, + storeContexts: [] as any[], + options: {}, + }, + }; + + return { + actions, + definitions, + defaultContext: 'MICROSCOPY', + }; +} diff --git a/extensions/dicom-microscopy/src/getPanelModule.tsx b/extensions/dicom-microscopy/src/getPanelModule.tsx new file mode 100644 index 000000000..ef49c9331 --- /dev/null +++ b/extensions/dicom-microscopy/src/getPanelModule.tsx @@ -0,0 +1,49 @@ +import React from 'react'; +import { ServicesManager, CommandsManager, ExtensionManager } from '@ohif/core'; +import { useViewportGrid } from '@ohif/ui'; +import MicroscopyPanel from './components/MicroscopyPanel/MicroscopyPanel'; + +// TODO: +// - No loading UI exists yet +// - cancel promises when component is destroyed +// - show errors in UI for thumbnails if promise fails + +export default function getPanelModule({ + commandsManager, + extensionManager, + servicesManager, +}: { + servicesManager: ServicesManager; + commandsManager: CommandsManager; + extensionManager: ExtensionManager; +}) { + const wrappedMeasurementPanel = () => { + const [ + { activeViewportIndex, viewports }, + viewportGridService, + ] = useViewportGrid(); + + return ( + {}} + onRejectComplete={() => {}} + commandsManager={commandsManager} + servicesManager={servicesManager} + extensionManager={extensionManager} + /> + ); + }; + + return [ + { + name: 'measure', + iconName: 'tab-linear', + iconLabel: 'Measure', + label: 'Measurements', + secondaryLabel: 'Measurements', + component: wrappedMeasurementPanel, + }, + ]; +} diff --git a/extensions/dicom-microscopy/src/helpers/formatDICOMDate.js b/extensions/dicom-microscopy/src/helpers/formatDICOMDate.js new file mode 100644 index 000000000..c048df472 --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/formatDICOMDate.js @@ -0,0 +1,11 @@ +import moment from 'moment'; + +/** + * Formats DICOM date. + * + * @param {string} date + * @param {string} strFormat + */ +export default function formatDICOMDate(date, strFormat = 'MMM D, YYYY') { + return moment(date, 'YYYYMMDD').format(strFormat); +} diff --git a/extensions/dicom-microscopy/src/helpers/formatDICOMDate.test.js b/extensions/dicom-microscopy/src/helpers/formatDICOMDate.test.js new file mode 100644 index 000000000..abb9b2c1f --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/formatDICOMDate.test.js @@ -0,0 +1,9 @@ +import formatDICOMDate from './formatDICOMDate'; + +describe('formatDICOMDate', () => { + it('should format DICOM date string', () => { + const date = '20180916'; + const formattedDate = formatDICOMDate(date); + expect(formattedDate).toEqual('Sep 16, 2018'); + }); +}); diff --git a/extensions/dicom-microscopy/src/helpers/formatDICOMPatientName.js b/extensions/dicom-microscopy/src/helpers/formatDICOMPatientName.js new file mode 100644 index 000000000..fd62d94c9 --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/formatDICOMPatientName.js @@ -0,0 +1,21 @@ +/** + * Formats a patient name for display purposes. + * + * @param {string} name DICOM patient name string + * @returns {string} formatted name + */ +export default function formatDICOMPatientName(name) { + if (typeof name !== 'string') return; + + /** + * Convert the first ^ to a ', '. String.replace() only affects + * the first appearance of the character. + */ + const commaBetweenFirstAndLast = name.replace('^', ', '); + + /** Replace any remaining '^' characters with spaces */ + const cleaned = commaBetweenFirstAndLast.replace(/\^/g, ' '); + + /** Trim any extraneous whitespace */ + return cleaned.trim(); +} diff --git a/extensions/dicom-microscopy/src/helpers/formatDICOMPatientName.test.js b/extensions/dicom-microscopy/src/helpers/formatDICOMPatientName.test.js new file mode 100644 index 000000000..efda1ed02 --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/formatDICOMPatientName.test.js @@ -0,0 +1,17 @@ +import formatDICOMPatientName from './formatDICOMPatientName'; + +describe('formatDICOMPatientName', () => { + it('should format DICOM patient name correctly', () => { + const patientName = 'Blackford^Test'; + const formattedPatientName = formatDICOMPatientName(patientName); + expect(formattedPatientName).toEqual('Blackford, Test'); + }); + + it('should return undefined it input is not a string', () => { + expect(formatDICOMPatientName(123)).toEqual(undefined); + expect(formatDICOMPatientName(null)).toEqual(undefined); + expect(formatDICOMPatientName(undefined)).toEqual(undefined); + expect(formatDICOMPatientName(false)).toEqual(undefined); + expect(formatDICOMPatientName([])).toEqual(undefined); + }); +}); diff --git a/extensions/dicom-microscopy/src/helpers/formatDICOMTime.js b/extensions/dicom-microscopy/src/helpers/formatDICOMTime.js new file mode 100644 index 000000000..ea2deb7df --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/formatDICOMTime.js @@ -0,0 +1,17 @@ +import moment from 'moment'; + +/** + * DICOM Time is stored as HHmmss.SSS, where: + * HH 24 hour time: + * m mm 0..59 Minutes + * s ss 0..59 Seconds + * S SS SSS 0..999 Fractional seconds + * + * Goal: '24:12:12' + * + * @param {*} time + * @param {string} strFormat + */ +export default function formatDICOMTime(time, strFormat = 'HH:mm:ss') { + return moment(time, 'HH:mm:ss').format(strFormat); +} diff --git a/extensions/dicom-microscopy/src/helpers/formatDICOMTime.test.js b/extensions/dicom-microscopy/src/helpers/formatDICOMTime.test.js new file mode 100644 index 000000000..a94d9bc83 --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/formatDICOMTime.test.js @@ -0,0 +1,9 @@ +import formatDICOMTime from './formatDICOMTime'; + +describe('formatDICOMTime', () => { + it('should format DICOM time string', () => { + const time = '101300.000'; + const formattedTime = formatDICOMTime(time); + expect(formattedTime).toEqual('10:13:00'); + }); +}); diff --git a/extensions/dicom-microscopy/src/helpers/formatNumberPrecision.js b/extensions/dicom-microscopy/src/helpers/formatNumberPrecision.js new file mode 100644 index 000000000..9aa152fe1 --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/formatNumberPrecision.js @@ -0,0 +1,9 @@ +/** + * Formats a number to a fixed precision. + * + * @param {number} number + * @param {number} precision + */ +export default function formatNumberPrecision(number, precision) { + return Number(parseFloat(number).toFixed(precision)); +} diff --git a/extensions/dicom-microscopy/src/helpers/formatNumberPrecision.test.js b/extensions/dicom-microscopy/src/helpers/formatNumberPrecision.test.js new file mode 100644 index 000000000..0ccce4d9e --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/formatNumberPrecision.test.js @@ -0,0 +1,9 @@ +import formatNumberPrecision from './formatNumberPrecision'; + +describe('formatNumberPrecision', () => { + it('should format number precision', () => { + const number = 0.229387; + const formattedNumber = formatNumberPrecision(number, 2); + expect(formattedNumber).toEqual(0.23); + }); +}); diff --git a/extensions/dicom-microscopy/src/helpers/index.js b/extensions/dicom-microscopy/src/helpers/index.js new file mode 100644 index 000000000..59468982c --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/index.js @@ -0,0 +1,15 @@ +import formatDICOMPatientName from './formatDICOMPatientName'; +import formatDICOMDate from './formatDICOMDate'; +import formatDICOMTime from './formatDICOMTime'; +import formatNumberPrecision from './formatNumberPrecision'; +import isValidNumber from './isValidNumber'; + +const helpers = { + formatDICOMPatientName, + formatDICOMDate, + formatDICOMTime, + formatNumberPrecision, + isValidNumber, +}; + +export default helpers; diff --git a/extensions/dicom-microscopy/src/helpers/isValidNumber.js b/extensions/dicom-microscopy/src/helpers/isValidNumber.js new file mode 100644 index 000000000..086b1c08a --- /dev/null +++ b/extensions/dicom-microscopy/src/helpers/isValidNumber.js @@ -0,0 +1,3 @@ +export default function isValidNumber(value) { + return typeof value === 'number' && !isNaN(value); +} diff --git a/extensions/dicom-microscopy/src/id.js b/extensions/dicom-microscopy/src/id.js new file mode 100644 index 000000000..ebe5acd98 --- /dev/null +++ b/extensions/dicom-microscopy/src/id.js @@ -0,0 +1,5 @@ +import packageJson from '../package.json'; + +const id = packageJson.name; + +export { id }; diff --git a/extensions/dicom-microscopy/src/index.tsx b/extensions/dicom-microscopy/src/index.tsx new file mode 100644 index 000000000..66dfeacd9 --- /dev/null +++ b/extensions/dicom-microscopy/src/index.tsx @@ -0,0 +1,117 @@ +import { id } from './id'; +import React, { Suspense } from 'react'; +import getPanelModule from './getPanelModule'; +import getCommandsModule from './getCommandsModule'; + +import { useViewportGrid } from '@ohif/ui'; +import getDicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler'; +import getDicomMicroscopySRSopClassHandler from './DicomMicroscopySRSopClassHandler'; +import MicroscopyService from './services/MicroscopyService'; + +const Component = React.lazy(() => { + return import('./DicomMicroscopyViewport'); +}); + +const MicroscopyViewport = props => { + return ( + Loading...
}> + + + ); +}; + +/** + * You can remove any of the following modules if you don't need them. + */ +export default { + /** + * Only required property. Should be a unique value across all extensions. + * You ID can be anything you want, but it should be unique. + */ + id, + + async preRegistration({ + servicesManager, + commandsManager, + configuration = {}, + appConfig, + }) { + servicesManager.registerService( + MicroscopyService.REGISTRATION(servicesManager) + ); + }, + + /** + * ViewportModule should provide a list of viewports that will be available in OHIF + * for Modes to consume and use in the viewports. Each viewport is defined by + * {name, component} object. Example of a viewport module is the CornerstoneViewport + * that is provided by the Cornerstone extension in OHIF. + */ + getViewportModule({ servicesManager, extensionManager, commandsManager }) { + /** + * + * @param props {*} + * @param props.displaySets + * @param props.viewportIndex + * @param props.viewportLabel + * @param props.dataSource + * @param props.viewportOptions + * @param props.displaySetOptions + * @returns + */ + const ExtendedMicroscopyViewport = props => { + const { viewportOptions } = props; + + const [viewportGrid, viewportGridService] = useViewportGrid(); + const { viewports, activeViewportIndex } = viewportGrid; + + return ( + { + viewportGridService.setActiveViewportIndex(viewportIndex); + }} + viewportData={viewportOptions} + {...props} + /> + ); + }; + + return [ + { + name: 'microscopy-dicom', + component: ExtendedMicroscopyViewport, + }, + ]; + }, + + /** + * SopClassHandlerModule should provide a list of sop class handlers that will be + * available in OHIF for Modes to consume and use to create displaySets from Series. + * Each sop class handler is defined by a { name, sopClassUids, getDisplaySetsFromSeries}. + * Examples include the default sop class handler provided by the default extension + */ + getSopClassHandlerModule({ + servicesManager, + commandsManager, + extensionManager, + }) { + return [ + getDicomMicroscopySopClassHandler({ + servicesManager, + extensionManager, + }), + getDicomMicroscopySRSopClassHandler({ + servicesManager, + extensionManager, + }), + ]; + }, + + getPanelModule, + + getCommandsModule, +}; diff --git a/extensions/dicom-microscopy/src/services/MicroscopyService.js b/extensions/dicom-microscopy/src/services/MicroscopyService.js new file mode 100644 index 000000000..d1ff76b5b --- /dev/null +++ b/extensions/dicom-microscopy/src/services/MicroscopyService.js @@ -0,0 +1,634 @@ +import ViewerManager, { EVENTS as ViewerEvents } from '../tools/viewerManager'; +import RoiAnnotation, { + EVENTS as AnnotationEvents, +} from '../utils/RoiAnnotation'; +import styles from '../utils/styles'; +import { DicomMetadataStore, PubSubService } from '@ohif/core'; + +const EVENTS = { + ANNOTATION_UPDATED: 'annotationUpdated', + ANNOTATION_SELECTED: 'annotationSelected', + ANNOTATION_REMOVED: 'annotationRemoved', + RELABEL: 'relabel', + DELETE: 'delete', +}; + +/** + * MicroscopyService is responsible to manage multiple third-party API's + * microscopy viewers expose methods to manage the interaction with these + * viewers and handle their ROI graphics to create, remove and modify the + * ROI annotations relevant to the application + */ +export default class MicroscopyService extends PubSubService { + public static REGISTRATION = serviceManager => { + return { + name: 'microscopyService', + altName: 'MicroscopyService', + create: ({ configuration = {} }) => { + return new MicroscopyService(serviceManager); + }, + }; + }; + + serviceManager: any; + + managedViewers = new Set(); + roiUids = new Set(); + annotations = {}; + selectedAnnotation = null; + pendingFocus = false; + + constructor(serviceManager) { + super(EVENTS); + this.serviceManager = serviceManager; + this._onRoiAdded = this._onRoiAdded.bind(this); + this._onRoiModified = this._onRoiModified.bind(this); + this._onRoiRemoved = this._onRoiRemoved.bind(this); + this._onRoiUpdated = this._onRoiUpdated.bind(this); + this._onRoiSelected = this._onRoiSelected.bind(this); + this.isROIsVisible = true; + } + + /** + * Cleares all the annotations and managed viewers, setting the manager state + * to its initial state + */ + clear() { + this.managedViewers.forEach(managedViewer => managedViewer.destroy()); + this.managedViewers.clear(); + for (var key in this.annotations) { + delete this.annotations[key]; + } + + this.roiUids.clear(); + this.selectedAnnotation = null; + this.pendingFocus = false; + } + + clearAnnotations() { + Object.keys(this.annotations).forEach(uid => { + this.removeAnnotation(this.annotations[uid]); + }); + } + + /** + * Observes when a ROI graphic is added, creating the correspondent annotation + * with the current graphic and view state. + * Creates a subscription for label updating for the created annotation and + * publishes an ANNOTATION_UPDATED event when it happens. + * Also triggers the relabel process after the graphic is placed. + * + * @param {Object} data The published data + * @param {Object} data.roiGraphic The added ROI graphic object + * @param {ViewerManager} data.managedViewer The origin viewer for the event + */ + _onRoiAdded(data) { + const { roiGraphic, managedViewer, label } = data; + const { studyInstanceUID, seriesInstanceUID } = managedViewer; + const viewState = managedViewer.getViewState(); + + const roiAnnotation = new RoiAnnotation( + roiGraphic, + studyInstanceUID, + seriesInstanceUID, + '', + viewState + ); + + this.roiUids.add(roiGraphic.uid); + this.annotations[roiGraphic.uid] = roiAnnotation; + + roiAnnotation.subscribe(AnnotationEvents.LABEL_UPDATED, () => { + this._broadcastEvent(EVENTS.ANNOTATION_UPDATED, roiAnnotation); + }); + + if (label !== undefined) { + roiAnnotation.setLabel(label); + } else { + const onRelabel = item => + managedViewer.updateROIProperties({ + uid: roiGraphic.uid, + properties: { label: item.label, finding: item.finding }, + }); + this.triggerRelabel(roiAnnotation, true, onRelabel); + } + } + + /** + * Observes when a ROI graphic is modified, updating the correspondent + * annotation with the current graphic and view state. + * + * @param {Object} data The published data + * @param {Object} data.roiGraphic The modified ROI graphic object + */ + _onRoiModified(data) { + const { roiGraphic, managedViewer } = data; + const roiAnnotation = this.getAnnotation(roiGraphic.uid); + if (!roiAnnotation) return; + roiAnnotation.setRoiGraphic(roiGraphic); + roiAnnotation.setViewState(managedViewer.getViewState()); + } + + /** + * Observes when a ROI graphic is removed, reflecting the removal in the + * annotations' state. + * + * @param {Object} data The published data + * @param {Object} data.roiGraphic The removed ROI graphic object + */ + _onRoiRemoved(data) { + const { roiGraphic } = data; + this.roiUids.delete(roiGraphic.uid); + this.annotations[roiGraphic.uid].destroy(); + delete this.annotations[roiGraphic.uid]; + this._broadcastEvent(EVENTS.ANNOTATION_REMOVED, roiGraphic); + } + + /** + * Observes any changes on ROI graphics and synchronize all the managed + * viewers to reflect those changes. + * Also publishes an ANNOTATION_UPDATED event to notify the subscribers. + * + * @param {Object} data The published data + * @param {Object} data.roiGraphic The added ROI graphic object + * @param {ViewerManager} data.managedViewer The origin viewer for the event + */ + _onRoiUpdated(data) { + const { roiGraphic, managedViewer } = data; + this.synchronizeViewers(managedViewer); + this._broadcastEvent(EVENTS.ANNOTATION_UPDATED, this.getAnnotation(roiGraphic.uid)); + } + + /** + * Observes when an ROI is selected. + * Also publishes an ANNOTATION_SELECTED event to notify the subscribers. + * + * @param {Object} data The published data + * @param {Object} data.roiGraphic The added ROI graphic object + * @param {ViewerManager} data.managedViewer The origin viewer for the event + */ + _onRoiSelected(data) { + const { roiGraphic } = data; + const selectedAnnotation = this.getAnnotation(roiGraphic.uid); + if (selectedAnnotation && selectedAnnotation !== this.getSelectedAnnotation()) { + if (this.selectedAnnotation) this.clearSelection(); + this.selectedAnnotation = selectedAnnotation; + this._broadcastEvent(EVENTS.ANNOTATION_SELECTED, selectedAnnotation); + } + } + + /** + * Creates the subscriptions for the managed viewer being added + * + * @param {ViewerManager} managedViewer The viewer being added + */ + _addManagedViewerSubscriptions(managedViewer) { + managedViewer._roiAddedSubscription = managedViewer.subscribe(ViewerEvents.ADDED, this._onRoiAdded); + managedViewer._roiModifiedSubscription = managedViewer.subscribe(ViewerEvents.MODIFIED, this._onRoiModified); + managedViewer._roiRemovedSubscription = managedViewer.subscribe(ViewerEvents.REMOVED, this._onRoiRemoved); + managedViewer._roiUpdatedSubscription = managedViewer.subscribe(ViewerEvents.UPDATED, this._onRoiUpdated); + managedViewer._roiSelectedSubscription = managedViewer.subscribe(ViewerEvents.UPDATED, this._onRoiSelected); + } + + /** + * Removes the subscriptions for the managed viewer being removed + * + * @param {ViewerManager} managedViewer The viewer being removed + */ + _removeManagedViewerSubscriptions(managedViewer) { + managedViewer._roiAddedSubscription && managedViewer._roiAddedSubscription.unsubscribe(); + managedViewer._roiModifiedSubscription && managedViewer._roiModifiedSubscription.unsubscribe(); + managedViewer._roiRemovedSubscription && managedViewer._roiRemovedSubscription.unsubscribe(); + managedViewer._roiUpdatedSubscription && managedViewer._roiUpdatedSubscription.unsubscribe(); + managedViewer._roiSelectedSubscription && managedViewer._roiSelectedSubscription.unsubscribe(); + + managedViewer._roiAddedSubscription = null; + managedViewer._roiModifiedSubscription = null; + managedViewer._roiRemovedSubscription = null; + managedViewer._roiUpdatedSubscription = null; + managedViewer._roiSelectedSubscription = null; + } + + /** + * Returns the managed viewers that are displaying the image with the given + * study and series UIDs + * + * @param {String} studyInstanceUID UID for the study + * @param {String} seriesInstanceUID UID for the series + * + * @returns {Array} The managed viewers for the given series UID + */ + _getManagedViewersForSeries(studyInstanceUID, seriesInstanceUID) { + const filter = managedViewer => + managedViewer.studyInstanceUID === studyInstanceUID && + managedViewer.seriesInstanceUID === seriesInstanceUID; + return Array.from(this.managedViewers).filter(filter); + } + + /** + * Returns the managed viewers that are displaying the image with the given + * study UID + * + * @param {String} studyInstanceUID UID for the study + * + * @returns {Array} The managed viewers for the given series UID + */ + getManagedViewersForStudy(studyInstanceUID) { + const filter = managedViewer => + managedViewer.studyInstanceUID === studyInstanceUID; + return Array.from(this.managedViewers).filter(filter); + } + + /** + * Restores the created annotations for the viewer being added + * + * @param {ViewerManager} managedViewer The viewer being added + */ + _restoreAnnotations(managedViewer) { + const { studyInstanceUID, seriesInstanceUID } = managedViewer; + const annotations = this.getAnnotationsForSeries( + studyInstanceUID, + seriesInstanceUID + ); + annotations.forEach(roiAnnotation => { + managedViewer.addRoiGraphic(roiAnnotation.roiGraphic); + }); + } + + /** + * Creates a managed viewer instance for the given thrid-party API's viewer. + * Restores existing annotations for the given study/series. + * Adds event subscriptions for the viewer being added. + * Focuses the selected annotation when the viewer is being loaded into the + * active viewport. + * + * @param {Object} viewer Third-party viewer API's object to be managed + * @param {Number} viewportIndex The index of the viewport to load the viewer + * @param {HTMLElement} container The DOM element where it will be renderd + * @param {String} studyInstanceUID The study UID of the loaded image + * @param {String} seriesInstanceUID The series UID of the loaded image + * @param {Array} displaySets All displaySets related to the same StudyInstanceUID + * + * @returns {ViewerManager} managed viewer + */ + addViewer( + viewer, + viewportIndex, + container, + studyInstanceUID, + seriesInstanceUID + ) { + const managedViewer = new ViewerManager( + viewer, + viewportIndex, + container, + studyInstanceUID, + seriesInstanceUID + ); + + this._restoreAnnotations(managedViewer); + viewer._manager = managedViewer; + this.managedViewers.add(managedViewer); + + // this._potentiallyLoadSR(studyInstanceUID, displaySets); + this._addManagedViewerSubscriptions(managedViewer); + + if (this.pendingFocus) { + this.pendingFocus = false; + this.focusAnnotation(this.selectedAnnotation, viewportIndex); + } + + return managedViewer; + } + + _potentiallyLoadSR(StudyInstanceUID, displaySets) { + const studyMetadata = DicomMetadataStore.getStudy(StudyInstanceUID); + const smDisplaySet = displaySets.find(ds => ds.Modality === 'SM'); + + const { FrameOfReferenceUID, othersFrameOfReferenceUID } = smDisplaySet; + + if (!studyMetadata) { + return; + } + + let derivedDisplaySets = FrameOfReferenceUID + ? displaySets.filter( + ds => + ds.ReferencedFrameOfReferenceUID === FrameOfReferenceUID || + // sometimes each depth instance has the different FrameOfReferenceID + othersFrameOfReferenceUID.includes(ds.ReferencedFrameOfReferenceUID) + ) + : []; + + if (!derivedDisplaySets.length) { + return; + } + + derivedDisplaySets = derivedDisplaySets.filter(ds => ds.Modality === 'SR'); + + if (derivedDisplaySets.some(ds => ds.isLoaded === true)) { + // Don't auto load + return; + } + + // find most recent and load it. + let recentDateTime = 0; + let recentDisplaySet = derivedDisplaySets[0]; + + derivedDisplaySets.forEach(ds => { + const dateTime = Number(`${ds.SeriesDate}${ds.SeriesTime}`); + if (dateTime > recentDateTime) { + recentDateTime = dateTime; + recentDisplaySet = ds; + } + }); + + recentDisplaySet.isLoading = true; + + recentDisplaySet.load(smDisplaySet); + } + + /** + * Removes the given third-party viewer API's object from the managed viewers + * and cleares all its event subscriptions + * + * @param {Object} viewer Third-party viewer API's object to be removed + */ + removeViewer(viewer) { + const managedViewer = viewer._manager; + + this._removeManagedViewerSubscriptions(managedViewer); + managedViewer.destroy(); + this.managedViewers.delete(managedViewer); + } + + /** + * Toggle ROIs visibility + */ + toggleROIsVisibility() { + this.isROIsVisible ? this.hideROIs() : this.showROIs; + this.isROIsVisible = !this.isROIsVisible; + } + + /** + * Hide all ROIs + */ + hideROIs() { + this.managedViewers.forEach(mv => mv.hideROIs()); + } + + /** Show all ROIs */ + showROIs() { + this.managedViewers.forEach(mv => mv.showROIs()); + } + + /** + * Returns a RoiAnnotation instance for the given ROI UID + * + * @param {String} uid UID of the annotation + * + * @returns {RoiAnnotation} The RoiAnnotation instance found for the given UID + */ + getAnnotation(uid) { + return this.annotations[uid]; + } + + /** + * Returns all the RoiAnnotation instances being managed + * + * @returns {Array} All RoiAnnotation instances + */ + getAnnotations() { + const annotations = []; + Object.keys(this.annotations).forEach(uid => { + annotations.push(this.getAnnotation(uid)); + }); + return annotations; + } + + /** + * Returns the RoiAnnotation instances registered with the given study UID + * + * @param {String} studyInstanceUID UID for the study + */ + getAnnotationsForStudy(studyInstanceUID) { + const filter = a => a.studyInstanceUID === studyInstanceUID; + return this.getAnnotations().filter(filter); + } + + /** + * Returns the RoiAnnotation instances registered with the given study and + * series UIDs + * + * @param {String} studyInstanceUID UID for the study + * @param {String} seriesInstanceUID UID for the series + */ + getAnnotationsForSeries(studyInstanceUID, seriesInstanceUID) { + const filter = annotation => + annotation.studyInstanceUID === studyInstanceUID && + annotation.seriesInstanceUID === seriesInstanceUID; + return this.getAnnotations().filter(filter); + } + + /** + * Returns the selected RoiAnnotation instance or null if none is selected + * + * @returns {RoiAnnotation} The selected RoiAnnotation instance + */ + getSelectedAnnotation() { + return this.selectedAnnotation; + } + + /** + * Clear current RoiAnnotation selection + */ + clearSelection() { + if (this.selectedAnnotation) { + this.setROIStyle(this.selectedAnnotation.uid, { + stroke: { + color: '#00ff00', + }, + }); + } + this.selectedAnnotation = null; + } + + /** + * Selects the given RoiAnnotation instance, publishing an ANNOTATION_SELECTED + * event to notify all the subscribers + * + * @param {RoiAnnotation} roiAnnotation The instance to be selected + */ + selectAnnotation(roiAnnotation) { + if (this.selectedAnnotation) this.clearSelection(); + + this.selectedAnnotation = roiAnnotation; + this._broadcastEvent(EVENTS.ANNOTATION_SELECTED, roiAnnotation); + this.setROIStyle(roiAnnotation.uid, styles.active); + } + + /** + * Toggles overview map + * + * @param viewportIndex The active viewport index + * @returns {void} + */ + toggleOverviewMap(viewportIndex) { + const managedViewers = Array.from(this.managedViewers); + const managedViewer = managedViewers.find( + mv => mv.viewportIndex === viewportIndex + ); + if (managedViewer) { + managedViewer.toggleOverviewMap(); + } + } + + /** + * Removes a RoiAnnotation instance from the managed annotations and reflects + * its removal on all third-party viewers being managed + * + * @param {RoiAnnotation} roiAnnotation The instance to be removed + */ + removeAnnotation(roiAnnotation) { + const { uid, studyInstanceUID, seriesInstanceUID } = roiAnnotation; + const filter = managedViewer => + managedViewer.studyInstanceUID === studyInstanceUID && + managedViewer.seriesInstanceUID === seriesInstanceUID; + + const managedViewers = Array.from(this.managedViewers).filter(filter); + + managedViewers.forEach(managedViewer => + managedViewer.removeRoiGraphic(uid) + ); + + if (this.annotations[uid]) { + this.roiUids.delete(uid); + this.annotations[uid].destroy(); + delete this.annotations[uid]; + + this._broadcastEvent(EVENTS.ANNOTATION_REMOVED, roiAnnotation); + } + } + + /** + * Focus the given RoiAnnotation instance by changing the OpenLayers' Map view + * state of the managed viewer with the given viewport index. + * If the image for the given annotation is not yet loaded into the viewport, + * it will set a pendingFocus flag to true in order to perform the focus when + * the managed viewer instance is created. + * + * @param {RoiAnnotation} roiAnnotation RoiAnnotation instance to be focused + * @param {Number} viewportIndex Index of the viewport to focus + */ + focusAnnotation(roiAnnotation, viewportIndex) { + const filter = mv => mv.viewportIndex === viewportIndex; + const managedViewer = Array.from(this.managedViewers).find(filter); + if (managedViewer) { + managedViewer.setViewStateByExtent(roiAnnotation); + } else { + this.pendingFocus = true; + } + } + + /** + * Synchronize the ROI graphics for all the managed viewers that has the same + * series UID of the given managed viewer + * + * @param {ViewerManager} baseManagedViewer Reference managed viewer + */ + synchronizeViewers(baseManagedViewer) { + const { studyInstanceUID, seriesInstanceUID } = baseManagedViewer; + const managedViewers = this._getManagedViewersForSeries( + studyInstanceUID, + seriesInstanceUID + ); + + // Prevent infinite loops arrising from updates. + managedViewers.forEach(managedViewer => + this._removeManagedViewerSubscriptions(managedViewer) + ); + + managedViewers.forEach(managedViewer => { + if (managedViewer === baseManagedViewer) { + return; + } + + const annotations = this.getAnnotationsForSeries( + studyInstanceUID, + seriesInstanceUID + ); + managedViewer.clearRoiGraphics(); + annotations.forEach(roiAnnotation => { + managedViewer.addRoiGraphic(roiAnnotation.roiGraphic); + }); + }); + + managedViewers.forEach(managedViewer => + this._addManagedViewerSubscriptions(managedViewer) + ); + } + + /** + * Activates interactions across all the viewers being managed + * + * @param {Array} interactions interactions + */ + activateInteractions(interactions) { + this.managedViewers.forEach(mv => mv.activateInteractions(interactions)); + this.activeInteractions = interactions; + } + + /** + * Triggers the relabelling process for the given RoiAnnotation instance, by + * publishing the RELABEL event to notify the subscribers + * + * @param {RoiAnnotation} roiAnnotation The instance to be relabelled + * @param {boolean} newAnnotation Whether the annotation is newly drawn (so it deletes on cancel). + */ + triggerRelabel(roiAnnotation, newAnnotation = false, onRelabel) { + if (!onRelabel) { + onRelabel = ({ label }) => + this.managedViewers.forEach(mv => + mv.updateROIProperties({ + uid: roiAnnotation.uid, + properties: { label }, + }) + ); + } + + this._broadcastEvent(EVENTS.RELABEL, { + roiAnnotation, + deleteCallback: () => this.removeAnnotation(roiAnnotation), + successCallback: onRelabel, + newAnnotation, + }); + } + + /** + * Triggers the deletion process for the given RoiAnnotation instance, by + * publishing the DELETE event to notify the subscribers + * + * @param {RoiAnnotation} roiAnnotation The instance to be deleted + */ + triggerDelete(roiAnnotation) { + this._broadcastEvent(EVENTS.DELETE, roiAnnotation); + } + + /** + * Set ROI style for all managed viewers + * + * @param {string} uid The ROI uid that will be styled + * @param {object} styleOptions - Style options + * @param {object*} styleOptions.stroke - Style options for the outline of the geometry + * @param {number[]} styleOptions.stroke.color - RGBA color of the outline + * @param {number} styleOptions.stroke.width - Width of the outline + * @param {object*} styleOptions.fill - Style options for body the geometry + * @param {number[]} styleOptions.fill.color - RGBA color of the body + * @param {object*} styleOptions.image - Style options for image + */ + setROIStyle(uid, styleOptions) { + this.managedViewers.forEach(mv => mv.setROIStyle(uid, styleOptions)); + } +} + +export { EVENTS }; diff --git a/extensions/dicom-microscopy/src/tools/viewerManager.js b/extensions/dicom-microscopy/src/tools/viewerManager.js new file mode 100644 index 000000000..bff7318d7 --- /dev/null +++ b/extensions/dicom-microscopy/src/tools/viewerManager.js @@ -0,0 +1,491 @@ +import coordinateFormatScoord3d2Geometry from '../utils/coordinateFormatScoord3d2Geometry'; +import styles from '../utils/styles'; + +import { PubSubService } from '@ohif/core'; + +// Events from the third-party viewer +const ApiEvents = { + /** Triggered when a ROI was added. */ + ROI_ADDED: 'dicommicroscopyviewer_roi_added', + /** Triggered when a ROI was modified. */ + ROI_MODIFIED: 'dicommicroscopyviewer_roi_modified', + /** Triggered when a ROI was removed. */ + ROI_REMOVED: 'dicommicroscopyviewer_roi_removed', + /** Triggered when a ROI was drawn. */ + ROI_DRAWN: `dicommicroscopyviewer_roi_drawn`, + /** Triggered when a ROI was selected. */ + ROI_SELECTED: `dicommicroscopyviewer_roi_selected`, + /** Triggered when a viewport move has started. */ + MOVE_STARTED: `dicommicroscopyviewer_move_started`, + /** Triggered when a viewport move has ended. */ + MOVE_ENDED: `dicommicroscopyviewer_move_ended`, + /** Triggered when a loading of data has started. */ + LOADING_STARTED: `dicommicroscopyviewer_loading_started`, + /** Triggered when a loading of data has ended. */ + LOADING_ENDED: `dicommicroscopyviewer_loading_ended`, + /** Triggered when an error occurs during loading of data. */ + LOADING_ERROR: `dicommicroscopyviewer_loading_error`, + /* Triggered when the loading of an image tile has started. */ + FRAME_LOADING_STARTED: `dicommicroscopyviewer_frame_loading_started`, + /* Triggered when the loading of an image tile has ended. */ + FRAME_LOADING_ENDED: `dicommicroscopyviewer_frame_loading_ended`, + /* Triggered when the error occurs during loading of an image tile. */ + FRAME_LOADING_ERROR: `dicommicroscopyviewer_frame_loading_ended`, +}; + +const EVENTS = { + ADDED: 'added', + MODIFIED: 'modified', + REMOVED: 'removed', + UPDATED: 'updated', + SELECTED: 'selected', +}; + +/** + * ViewerManager encapsulates the complexity of the third-party viewer and + * expose only the features/behaviors that are relevant to the application + */ +class ViewerManager extends PubSubService { + constructor( + viewer, + viewportIndex, + container, + studyInstanceUID, + seriesInstanceUID + ) { + super(EVENTS); + this.viewer = viewer; + this.viewportIndex = viewportIndex; + this.container = container; + this.studyInstanceUID = studyInstanceUID; + this.seriesInstanceUID = seriesInstanceUID; + + this.onRoiAdded = this.roiAddedHandler.bind(this); + this.onRoiModified = this.roiModifiedHandler.bind(this); + this.onRoiRemoved = this.roiRemovedHandler.bind(this); + this.onRoiSelected = this.roiSelectedHandler.bind(this); + this.contextMenuCallback = () => {}; + + // init symbols + const symbols = Object.getOwnPropertySymbols(this.viewer); + this._drawingSource = symbols.find(p => p.description === 'drawingSource'); + this._pyramid = symbols.find(p => p.description === 'pyramid'); + this._map = symbols.find(p => p.description === 'map'); + this._affine = symbols.find(p => p.description === 'affine'); + + this.registerEvents(); + this.activateDefaultInteractions(); + } + + addContextMenuCallback(callback) { + this.contextMenuCallback = callback; + } + + /** + * Destroys this managed viewer instance, clearing all the event handlers + */ + destroy() { + this.unregisterEvents(); + } + + /** + * This is to overrides the _broadcastEvent method of PubSubService and always + * send the ROI graphic object and this managed viewer instance. + * Due to the way that PubSubService is written, the same name override of the + * function doesn't work. + * + * @param {String} key key Subscription key + * @param {Object} roiGraphic ROI graphic object created by the third-party API + */ + publish(key, roiGraphic) { + this._broadcastEvent(key, { + roiGraphic, + managedViewer: this, + }); + } + + /** + * Registers all the relevant event handlers for the third-party API + */ + registerEvents() { + this.container.addEventListener(ApiEvents.ROI_ADDED, this.onRoiAdded); + this.container.addEventListener(ApiEvents.ROI_MODIFIED, this.onRoiModified); + this.container.addEventListener(ApiEvents.ROI_REMOVED, this.onRoiRemoved); + this.container.addEventListener(ApiEvents.ROI_SELECTED, this.onRoiSelected); + } + + /** + * Cleares all the relevant event handlers for the third-party API + */ + unregisterEvents() { + this.container.removeEventListener(ApiEvents.ROI_ADDED, this.onRoiAdded); + this.container.removeEventListener( + ApiEvents.ROI_MODIFIED, + this.onRoiModified + ); + this.container.removeEventListener( + ApiEvents.ROI_REMOVED, + this.onRoiRemoved + ); + this.container.removeEventListener( + ApiEvents.ROI_SELECTED, + this.onRoiSelected + ); + } + + /** + * Handles the ROI_ADDED event triggered by the third-party API + * + * @param {Event} event Event triggered by the third-party API + */ + roiAddedHandler(event) { + const roiGraphic = event.detail.payload; + this.publish(EVENTS.ADDED, roiGraphic); + this.publish(EVENTS.UPDATED, roiGraphic); + } + + /** + * Handles the ROI_MODIFIED event triggered by the third-party API + * + * @param {Event} event Event triggered by the third-party API + */ + roiModifiedHandler(event) { + const roiGraphic = event.detail.payload; + this.publish(EVENTS.MODIFIED, roiGraphic); + this.publish(EVENTS.UPDATED, roiGraphic); + } + + /** + * Handles the ROI_REMOVED event triggered by the third-party API + * + * @param {Event} event Event triggered by the third-party API + */ + roiRemovedHandler(event) { + const roiGraphic = event.detail.payload; + this.publish(EVENTS.REMOVED, roiGraphic); + this.publish(EVENTS.UPDATED, roiGraphic); + } + + /** + * Handles the ROI_SELECTED event triggered by the third-party API + * + * @param {Event} event Event triggered by the third-party API + */ + roiSelectedHandler(event) { + const roiGraphic = event.detail.payload; + this.publish(EVENTS.SELECTED, roiGraphic); + } + + /** + * Run the given callback operation without triggering any events for this + * instance, so subscribers will not be affected + * + * @param {Function} callback Callback that will run sinlently + */ + runSilently(callback) { + this.unregisterEvents(); + callback(); + this.registerEvents(); + } + + /** + * Removes all the ROI graphics from the third-party API + */ + clearRoiGraphics() { + this.runSilently(() => this.viewer.removeAllROIs()); + } + + showROIs() { + this.viewer.showROIs(); + } + + hideROIs() { + this.viewer.hideROIs(); + } + + /** + * Adds the given ROI graphic into the third-party API + * + * @param {Object} roiGraphic ROI graphic object to be added + */ + addRoiGraphic(roiGraphic) { + this.runSilently(() => this.viewer.addROI(roiGraphic, styles.default)); + } + + /** + * Adds the given ROI graphic into the third-party API, and also add a label. + * Used for importing from SR. + * + * @param {Object} roiGraphic ROI graphic object to be added. + * @param {String} label The label of the annotation. + */ + addRoiGraphicWithLabel(roiGraphic, label) { + // NOTE: Dicom Microscopy Viewer will override styles for "Text" evalutations + // to hide all other geometries, we are not going to use its label. + // if (label) { + // if (!roiGraphic.properties) roiGraphic.properties = {}; + // roiGraphic.properties.label = label; + // } + this.runSilently(() => this.viewer.addROI(roiGraphic, styles.default)); + + this._broadcastEvent(EVENTS.ADDED, { + roiGraphic, + managedViewer: this, + label, + }); + } + + /** + * Sets ROI style + * + * @param {String} uid ROI graphic UID to be styled + * @param {object} styleOptions - Style options + * @param {object} styleOptions.stroke - Style options for the outline of the geometry + * @param {number[]} styleOptions.stroke.color - RGBA color of the outline + * @param {number} styleOptions.stroke.width - Width of the outline + * @param {object} styleOptions.fill - Style options for body the geometry + * @param {number[]} styleOptions.fill.color - RGBA color of the body + * @param {object} styleOptions.image - Style options for image + */ + setROIStyle(uid, styleOptions) { + this.viewer.setROIStyle(uid, styleOptions); + } + + /** + * Removes the ROI graphic with the given UID from the third-party API + * + * @param {String} uid ROI graphic UID to be removed + */ + removeRoiGraphic(uid) { + this.viewer.removeROI(uid); + } + + /** + * Update properties of regions of interest. + * + * @param {object} roi - ROI to be updated + * @param {string} roi.uid - Unique identifier of the region of interest + * @param {object} roi.properties - ROI properties + * @returns {void} + */ + updateROIProperties({ uid, properties }) { + this.viewer.updateROI({ uid, properties }); + } + + /** + * Toggles overview map + * + * @returns {void} + */ + toggleOverviewMap() { + this.viewer.toggleOverviewMap(); + } + + /** + * Activates the viewer default interactions + * @returns {void} + */ + activateDefaultInteractions() { + /** Disable browser's native context menu inside the canvas */ + document.querySelector('.DicomMicroscopyViewer').addEventListener( + 'contextmenu', + event => { + event.preventDefault(); + // comment out when context menu for microscopy is enabled + // if (typeof this.contextMenuCallback === 'function') { + // this.contextMenuCallback(event); + // } + }, + false + ); + const defaultInteractions = [ + [ + 'dragPan', + { + bindings: { + mouseButtons: ['middle'], + }, + }, + ], + [ + 'dragZoom', + { + bindings: { + mouseButtons: ['right'], + }, + }, + ], + ['modify', {}], + ]; + this.activateInteractions(defaultInteractions); + } + + /** + * Activates interactions + * @param {Array} interactions Interactions to be activated + * @returns {void} + */ + activateInteractions(interactions) { + const interactionsMap = { + draw: activate => + activate ? 'activateDrawInteraction' : 'deactivateDrawInteraction', + modify: activate => + activate ? 'activateModifyInteraction' : 'deactivateModifyInteraction', + translate: activate => + activate + ? 'activateTranslateInteraction' + : 'deactivateTranslateInteraction', + snap: activate => + activate ? 'activateSnapInteraction' : 'deactivateSnapInteraction', + dragPan: activate => + activate + ? 'activateDragPanInteraction' + : 'deactivateDragPanInteraction', + dragZoom: activate => + activate + ? 'activateDragZoomInteraction' + : 'deactivateDragZoomInteraction', + select: activate => + activate ? 'activateSelectInteraction' : 'deactivateSelectInteraction', + }; + + const availableInteractionsName = Object.keys(interactionsMap); + availableInteractionsName.forEach(availableInteractionName => { + const interaction = interactions.find( + interaction => interaction[0] === availableInteractionName + ); + if (!interaction) { + const deactivateInteractionMethod = interactionsMap[ + availableInteractionName + ](false); + this.viewer[deactivateInteractionMethod](); + } else { + const [name, config] = interaction; + const activateInteractionMethod = interactionsMap[name](true); + this.viewer[activateInteractionMethod](config); + } + }); + } + + /** + * Accesses the internals of third-party API and returns the OpenLayers Map + * + * @returns {Object} OpenLayers Map component instance + */ + _getMapView() { + const map = this._getMap(); + return map.getView(); + } + + _getMap() { + const symbols = Object.getOwnPropertySymbols(this.viewer); + const _map = symbols.find(s => String(s) === 'Symbol(map)'); + window['map'] = this.viewer[_map]; + return this.viewer[_map]; + } + + /** + * Returns the current state for the OpenLayers View + * + * @returns {Object} Current view state + */ + getViewState() { + const view = this._getMapView(); + return { + center: view.getCenter(), + resolution: view.getResolution(), + zoom: view.getZoom(), + }; + } + + /** + * Sets the current state for the OpenLayers View + * + * @param {Object} viewState View state to be applied + */ + setViewState(viewState) { + const view = this._getMapView(); + + view.setZoom(viewState.zoom); + view.setResolution(viewState.resolution); + view.setCenter(viewState.center); + } + + setViewStateByExtent(roiAnnotation) { + const coordinates = roiAnnotation.getCoordinates(); + + if (Array.isArray(coordinates[0]) && !coordinates[2]) { + this._jumpToPolyline(coordinates); + } else if (Array.isArray(coordinates[0])) { + this._jumpToPolygonOrEllipse(coordinates); + } else { + this._jumpToPoint(coordinates); + } + } + + _jumpToPoint(coord) { + const pyramid = this.viewer[this._pyramid].metadata; + + const mappedCoord = coordinateFormatScoord3d2Geometry(coord, pyramid); + const view = this._getMapView(); + + view.setCenter(mappedCoord); + } + + _jumpToPolyline(coord) { + const pyramid = this.viewer[this._pyramid].metadata; + + const mappedCoord = coordinateFormatScoord3d2Geometry(coord, pyramid); + const view = this._getMapView(); + + const x = mappedCoord[0]; + const y = mappedCoord[1]; + + const xab = (x[0] + y[0]) / 2; + const yab = (x[1] + y[1]) / 2; + const midpoint = [xab, yab]; + + view.setCenter(midpoint); + } + + _jumpToPolygonOrEllipse(coordinates) { + const pyramid = this.viewer[this._pyramid].metadata; + + let minX = Infinity; + let maxX = -Infinity; + let minY = Infinity; + let maxY = -Infinity; + + coordinates.forEach(coord => { + let mappedCoord = coordinateFormatScoord3d2Geometry(coord, pyramid); + + const [x, y] = mappedCoord; + if (x < minX) { + minX = x; + } else if (x > maxX) { + maxX = x; + } + + if (y < minY) { + minY = y; + } else if (y > maxY) { + maxY = y; + } + }); + + const width = maxX - minX; + const height = maxY - minY; + + minX -= 0.5 * width; + maxX += 0.5 * width; + minY -= 0.5 * height; + maxY += 0.5 * height; + + const map = this._getMap(); + map.getView().fit([minX, minY, maxX, maxY], map.getSize()); + } +} + +export { EVENTS }; + +export default ViewerManager; diff --git a/extensions/dicom-microscopy/src/utils/DEVICE_OBSERVER_UID.js b/extensions/dicom-microscopy/src/utils/DEVICE_OBSERVER_UID.js new file mode 100644 index 000000000..cb3585870 --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/DEVICE_OBSERVER_UID.js @@ -0,0 +1,5 @@ +// We need to define a UID for this extension as a device, and it should be the same for all saves: + +const uid = '2.25.285241207697168520771311899641885187923'; + +export default uid; diff --git a/extensions/dicom-microscopy/src/utils/RoiAnnotation.js b/extensions/dicom-microscopy/src/utils/RoiAnnotation.js new file mode 100644 index 000000000..e8ca04021 --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/RoiAnnotation.js @@ -0,0 +1,196 @@ +import areaOfPolygon from './areaOfPolygon'; + +import { PubSubService } from '@ohif/core'; + +const EVENTS = { + LABEL_UPDATED: 'labelUpdated', + GRAPHIC_UPDATED: 'graphicUpdated', + VIEW_UPDATED: 'viewUpdated', + REMOVED: 'removed', +}; + +/** + * Represents a single annotation for the Microscopy Viewer + */ +class RoiAnnotation extends PubSubService { + constructor( + roiGraphic, + studyInstanceUID, + seriesInstanceUID, + label = '', + viewState = null + ) { + super(EVENTS); + this.uid = roiGraphic.uid; + this.roiGraphic = roiGraphic; + this.studyInstanceUID = studyInstanceUID; + this.seriesInstanceUID = seriesInstanceUID; + this.label = label; + this.viewState = viewState; + this.setMeasurements(roiGraphic); + } + + getScoord3d() { + const roiGraphic = this.roiGraphic; + + const roiGraphicSymbols = Object.getOwnPropertySymbols(roiGraphic); + const _scoord3d = roiGraphicSymbols.find( + s => String(s) === 'Symbol(scoord3d)' + ); + + return roiGraphic[_scoord3d]; + } + + getCoordinates() { + const scoord3d = this.getScoord3d(); + const scoord3dSymbols = Object.getOwnPropertySymbols(scoord3d); + + const _coordinates = scoord3dSymbols.find( + s => String(s) === 'Symbol(coordinates)' + ); + + const coordinates = scoord3d[_coordinates]; + return coordinates; + } + + /** + * When called will trigger the REMOVED event + */ + destroy() { + this._broadcastEvent(EVENTS.REMOVED, this); + } + + /** + * Updates the ROI graphic for the annotation and triggers the GRAPHIC_UPDATED + * event + * + * @param {Object} roiGraphic + */ + setRoiGraphic(roiGraphic) { + this.roiGraphic = roiGraphic; + this.setMeasurements(); + this._broadcastEvent(EVENTS.GRAPHIC_UPDATED, this); + } + + /** + * Update ROI measurement values based on its scoord3d coordinates. + * + * @returns {void} + */ + setMeasurements() { + const type = this.roiGraphic.scoord3d.graphicType; + const coordinates = this.roiGraphic.scoord3d.graphicData; + + switch (type) { + case 'ELLIPSE': + // This is a circle so only need one side + const point1 = coordinates[0]; + const point2 = coordinates[1]; + + let xLength2 = point2[0] - point1[0]; + let yLength2 = point2[1] - point1[1]; + + xLength2 *= xLength2; + yLength2 *= yLength2; + + const length = Math.sqrt(xLength2 + yLength2); + const radius = length / 2; + + const areaEllipse = Math.PI * radius * radius; + this._area = areaEllipse; + this._length = undefined; + break; + + case 'POLYGON': + const areaPolygon = areaOfPolygon(coordinates); + this._area = areaPolygon; + this._length = undefined; + break; + + case 'POINT': + this._area = undefined; + this._length = undefined; + break; + + case 'POLYLINE': + let len = 0; + for (let i = 1; i < coordinates.length; i++) { + const p1 = coordinates[i - 1]; + const p2 = coordinates[i]; + + let xLen = p2[0] - p1[0]; + let yLen = p2[1] - p1[1]; + + xLen *= xLen; + yLen *= yLen; + len += Math.sqrt(xLen + yLen); + } + + this._area = undefined; + this._length = len; + break; + } + } + + /** + * Update the OpenLayer Map's view state for the annotation and triggers the + * VIEW_UPDATED event + * + * @param {Object} viewState The new view state for the annotation + */ + setViewState(viewState) { + this.viewState = viewState; + this._broadcastEvent(EVENTS.VIEW_UPDATED, this); + } + + /** + * Update the label for the annotation and triggers the LABEL_UPDATED event + * + * @param {String} label New label for the annotation + */ + setLabel(label, finding) { + this.label = label || (finding && finding.CodeMeaning); + this.finding = finding || { + CodingSchemeDesignator: '@ohif/extension-dicom-microscopy', + CodeValue: label, + CodeMeaning: label, + }; + this._broadcastEvent(EVENTS.LABEL_UPDATED, this); + } + + /** + * Returns the geometry type of the annotation concatenated with the label + * defined for the annotation. + * Difference with getDetailedLabel() is that this will return empty string for empy + * label. + * + * @returns {String} Text with geometry type and label + */ + getLabel() { + const label = this.label ? `${this.label}` : ''; + return label; + } + + /** + * Returns the geometry type of the annotation concatenated with the label + * defined for the annotation + * + * @returns {String} Text with geometry type and label + */ + getDetailedLabel() { + const label = this.label ? `${this.label}` : '(empty)'; + return label; + } + + getLength() { + return this._length; + } + + getArea() { + return this._area; + } +} + +export { EVENTS }; + +export default RoiAnnotation; diff --git a/extensions/dicom-microscopy/src/utils/areaOfPolygon.js b/extensions/dicom-microscopy/src/utils/areaOfPolygon.js new file mode 100644 index 000000000..91a68c9ae --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/areaOfPolygon.js @@ -0,0 +1,17 @@ +export default function areaOfPolygon(coordinates) { + // Shoelace algorithm. + const n = coordinates.length; + let area = 0.0; + let j = n - 1; + + for (let i = 0; i < n; i++) { + area += + (coordinates[j][0] + coordinates[i][0]) * + (coordinates[j][1] - coordinates[i][1]); + j = i; // j is previous vertex to i + } + + // Return absolute value of half the sum + // (The value is halved as we are summing up triangles, not rectangles). + return Math.abs(area / 2.0); +} diff --git a/extensions/dicom-microscopy/src/utils/callInputDialog.tsx b/extensions/dicom-microscopy/src/utils/callInputDialog.tsx new file mode 100644 index 000000000..bffc2a627 --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/callInputDialog.tsx @@ -0,0 +1,75 @@ +import React from 'react'; +import { Input, Dialog } from '@ohif/ui'; + +/** + * + * @param {*} data + * @param {*} data.text + * @param {*} data.label + * @param {*} event + * @param {func} callback + * @param {*} isArrowAnnotateInputDialog + */ +export default function callInputDialog({ + uiDialogService, + title = 'Enter your annotation', + defaultValue = '', + callback = (value: string, action: string) => {} +}) { + const dialogId = 'microscopy-input-dialog'; + + const onSubmitHandler = ({ action, value }) => { + switch (action.id) { + case 'save': + callback(value.value, action.id); + break; + case 'cancel': + callback('', action.id); + break; + } + uiDialogService.dismiss({ id: dialogId }); + }; + + if (uiDialogService) { + uiDialogService.create({ + id: dialogId, + centralize: true, + isDraggable: false, + showOverlay: true, + content: Dialog, + contentProps: { + title: title, + value: { value: defaultValue }, + noCloseButton: true, + onClose: () => uiDialogService.dismiss({ id: dialogId }), + actions: [ + { id: 'cancel', text: 'Cancel', type: 'primary' }, + { id: 'save', text: 'Save', type: 'secondary' }, + ], + onSubmit: onSubmitHandler, + body: ({ value, setValue }) => { + return ( +
+ { + event.persist(); + setValue(value => ({ ...value, value: event.target.value })); + }} + onKeyPress={event => { + if (event.key === 'Enter') { + onSubmitHandler({ value, action: { id: 'save' } }); + } + }} + /> +
+ ); + }, + }, + }); + } +} \ No newline at end of file diff --git a/extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts b/extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts new file mode 100644 index 000000000..91d72e3e2 --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts @@ -0,0 +1,63 @@ +function isPrimitive(v: any) { + return !(typeof v == 'object' || Array.isArray(v)); +} + +const vrNumerics = [ + 'DS', + 'FL', + 'FD', + 'IS', + 'OD', + 'OF', + 'OL', + 'OV', + 'SL', + 'SS', + 'SV', + 'UL', + 'US', + 'UV', +]; + +/** + * Specialized for DICOM JSON format dataset cleaning. + * @param obj + * @returns + */ +export default function cleanDenaturalizedDataset(obj: any): any { + if (Array.isArray(obj)) { + const newAry = obj.map(o => + isPrimitive(o) ? o : cleanDenaturalizedDataset(o) + ); + return newAry; + } else if (isPrimitive(obj)) { + return obj; + } else { + Object.keys(obj).forEach(key => { + if (obj[key].Value === null && obj[key].vr) { + delete obj[key].Value; + } else if (Array.isArray(obj[key].Value) && obj[key].vr) { + if (obj[key].Value.length === 1 && obj[key].Value[0].BulkDataURI) { + obj[key].BulkDataURI = obj[key].Value[0].BulkDataURI; + + // prevent mixed-content blockage + if ( + window.location.protocol === 'https:' && + obj[key].BulkDataURI.startsWith('http:') + ) { + obj[key].BulkDataURI = obj[key].BulkDataURI.replace( + 'http:', + 'https:' + ); + } + delete obj[key].Value; + } else if (vrNumerics.includes(obj[key].vr)) { + obj[key].Value = obj[key].Value.map(v => +v); + } else { + obj[key].Value = obj[key].Value.map(cleanDenaturalizedDataset); + } + } + }); + return obj; + } +} diff --git a/extensions/dicom-microscopy/src/utils/constructSR.ts b/extensions/dicom-microscopy/src/utils/constructSR.ts new file mode 100644 index 000000000..ff78f13fe --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/constructSR.ts @@ -0,0 +1,213 @@ +import dcmjs from 'dcmjs'; +import DEVICE_OBSERVER_UID from './DEVICE_OBSERVER_UID'; + +/** + * + * @param {*} metadata - Microscopy Image instance metadata + * @param {*} SeriesDescription - SR description + * @param {*} annotations - Annotations + * + * @return Comprehensive3DSR dataset + */ +export default function constructSR( + metadata, + { SeriesDescription, SeriesNumber }, + annotations +) { + // Handle malformed data + if (!metadata.SpecimenDescriptionSequence) { + metadata.SpecimenDescriptionSequence = { + SpecimenUID: metadata.SeriesInstanceUID, + SpecimenIdentifier: metadata.SeriesDescription, + }; + } + const { SpecimenDescriptionSequence } = metadata; + + // construct Comprehensive3DSR dataset + const observationContext = new dcmjs.sr.templates.ObservationContext({ + observerPersonContext: new dcmjs.sr.templates.ObserverContext({ + observerType: new dcmjs.sr.coding.CodedConcept({ + value: '121006', + schemeDesignator: 'DCM', + meaning: 'Person', + }), + observerIdentifyingAttributes: new dcmjs.sr.templates.PersonObserverIdentifyingAttributes( + { + name: '@ohif/extension-dicom-microscopy', + } + ), + }), + observerDeviceContext: new dcmjs.sr.templates.ObserverContext({ + observerType: new dcmjs.sr.coding.CodedConcept({ + value: '121007', + schemeDesignator: 'DCM', + meaning: 'Device', + }), + observerIdentifyingAttributes: new dcmjs.sr.templates.DeviceObserverIdentifyingAttributes( + { + uid: DEVICE_OBSERVER_UID, + } + ), + }), + subjectContext: new dcmjs.sr.templates.SubjectContext({ + subjectClass: new dcmjs.sr.coding.CodedConcept({ + value: '121027', + schemeDesignator: 'DCM', + meaning: 'Specimen', + }), + subjectClassSpecificContext: new dcmjs.sr.templates.SubjectContextSpecimen( + { + uid: SpecimenDescriptionSequence.SpecimenUID, + identifier: + SpecimenDescriptionSequence.SpecimenIdentifier || + metadata.SeriesInstanceUID, + containerIdentifier: + metadata.ContainerIdentifier || metadata.SeriesInstanceUID, + } + ), + }), + }); + + const imagingMeasurements = []; + for (let i = 0; i < annotations.length; i++) { + const { roiGraphic: roi, label } = annotations[i]; + let { + measurements, + evaluations, + marker, + presentationState, + } = roi.properties; + + console.debug('[SR] storing marker...', marker); + console.debug('[SR] storing measurements...', measurements); + console.debug('[SR] storing evaluations...', evaluations); + console.debug('[SR] storing presentation state...', presentationState); + + if (presentationState) presentationState.marker = marker; + + /** Avoid incompatibility with dcmjs */ + measurements = measurements.map((measurement: any) => { + const ConceptName = Array.isArray(measurement.ConceptNameCodeSequence) + ? measurement.ConceptNameCodeSequence[0] + : measurement.ConceptNameCodeSequence; + + const MeasuredValue = Array.isArray(measurement.MeasuredValueSequence) + ? measurement.MeasuredValueSequence[0] + : measurement.MeasuredValueSequence; + + const MeasuredValueUnits = Array.isArray( + MeasuredValue.MeasurementUnitsCodeSequence + ) + ? MeasuredValue.MeasurementUnitsCodeSequence[0] + : MeasuredValue.MeasurementUnitsCodeSequence; + + return new dcmjs.sr.valueTypes.NumContentItem({ + name: new dcmjs.sr.coding.CodedConcept({ + meaning: ConceptName.CodeMeaning, + value: ConceptName.CodeValue, + schemeDesignator: ConceptName.CodingSchemeDesignator, + }), + value: MeasuredValue.NumericValue, + unit: new dcmjs.sr.coding.CodedConcept({ + value: MeasuredValueUnits.CodeValue, + meaning: MeasuredValueUnits.CodeMeaning, + schemeDesignator: MeasuredValueUnits.CodingSchemeDesignator, + }), + }); + }); + + /** Avoid incompatibility with dcmjs */ + evaluations = evaluations.map((evaluation: any) => { + const ConceptName = Array.isArray(evaluation.ConceptNameCodeSequence) + ? evaluation.ConceptNameCodeSequence[0] + : evaluation.ConceptNameCodeSequence; + + return new dcmjs.sr.valueTypes.TextContentItem({ + name: new dcmjs.sr.coding.CodedConcept({ + value: ConceptName.CodeValue, + meaning: ConceptName.CodeMeaning, + schemeDesignator: ConceptName.CodingSchemeDesignator, + }), + value: evaluation.TextValue, + relationshipType: evaluation.RelationshipType, + }); + }); + + const identifier = `ROI #${i + 1}`; + const group = new dcmjs.sr.templates.PlanarROIMeasurementsAndQualitativeEvaluations( + { + trackingIdentifier: new dcmjs.sr.templates.TrackingIdentifier({ + uid: roi.uid, + identifier: presentationState + ? identifier.concat(`(${JSON.stringify(presentationState)})`) + : identifier, + }), + referencedRegion: new dcmjs.sr.contentItems.ImageRegion3D({ + graphicType: roi.scoord3d.graphicType, + graphicData: roi.scoord3d.graphicData, + frameOfReferenceUID: roi.scoord3d.frameOfReferenceUID, + }), + findingType: new dcmjs.sr.coding.CodedConcept({ + value: label, + schemeDesignator: '@ohif/extension-dicom-microscopy', + meaning: 'FREETEXT', + }), + /** Evaluations will conflict with current tracking identifier */ + /** qualitativeEvaluations: evaluations, */ + measurements, + } + ); + imagingMeasurements.push(...group); + } + + const measurementReport = new dcmjs.sr.templates.MeasurementReport({ + languageOfContentItemAndDescendants: new dcmjs.sr.templates.LanguageOfContentItemAndDescendants( + {} + ), + observationContext, + procedureReported: new dcmjs.sr.coding.CodedConcept({ + value: '112703', + schemeDesignator: 'DCM', + meaning: 'Whole Slide Imaging', + }), + imagingMeasurements, + }); + + const dataset = new dcmjs.sr.documents.Comprehensive3DSR({ + content: measurementReport[0], + evidence: [metadata], + seriesInstanceUID: dcmjs.data.DicomMetaDictionary.uid(), + seriesNumber: SeriesNumber, + seriesDescription: + SeriesDescription || 'Whole slide imaging structured report', + sopInstanceUID: dcmjs.data.DicomMetaDictionary.uid(), + instanceNumber: 1, + manufacturer: 'dcmjs-org', + }); + dataset.SpecificCharacterSet = 'ISO_IR 192'; + const fileMetaInformationVersionArray = new Uint8Array(2); + fileMetaInformationVersionArray[1] = 1; + + dataset._meta = { + FileMetaInformationVersion: { + Value: [fileMetaInformationVersionArray.buffer], // TODO + vr: 'OB', + }, + MediaStorageSOPClassUID: dataset.sopClassUID, + MediaStorageSOPInstanceUID: dataset.sopInstanceUID, + TransferSyntaxUID: { + Value: ['1.2.840.10008.1.2.1'], + vr: 'UI', + }, + ImplementationClassUID: { + Value: [dcmjs.data.DicomMetaDictionary.uid()], + vr: 'UI', + }, + ImplementationVersionName: { + Value: ['@ohif/extension-dicom-microscopy'], + vr: 'SH', + }, + }; + + return dataset; +} diff --git a/extensions/dicom-microscopy/src/utils/coordinateFormatScoord3d2Geometry.js b/extensions/dicom-microscopy/src/utils/coordinateFormatScoord3d2Geometry.js new file mode 100644 index 000000000..70b6e42d5 --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/coordinateFormatScoord3d2Geometry.js @@ -0,0 +1,110 @@ +import { inv, multiply } from 'mathjs'; + +// TODO -> This is pulled out of some internal logic from Dicom Microscopy Viewer, +// We should likely just expose this there. + +export default function coordinateFormatScoord3d2Geometry( + coordinates, + pyramid +) { + let transform = false; + if (!Array.isArray(coordinates[0])) { + coordinates = [coordinates]; + transform = true; + } + const metadata = pyramid[pyramid.length - 1]; + const orientation = metadata.ImageOrientationSlide; + const spacing = _getPixelSpacing(metadata); + const origin = metadata.TotalPixelMatrixOriginSequence[0]; + const offset = [ + Number(origin.XOffsetInSlideCoordinateSystem), + Number(origin.YOffsetInSlideCoordinateSystem), + ]; + + coordinates = coordinates.map(c => { + const slideCoord = [c[0], c[1]]; + const pixelCoord = mapSlideCoord2PixelCoord({ + offset, + orientation, + spacing, + point: slideCoord, + }); + return [pixelCoord[0], -(pixelCoord[1] + 1), 0]; + }); + if (transform) { + return coordinates[0]; + } + return coordinates; +} + +function _getPixelSpacing(metadata) { + if (metadata.PixelSpacing) return metadata.PixelSpacing; + const functionalGroup = metadata.SharedFunctionalGroupsSequence[0]; + const pixelMeasures = functionalGroup.PixelMeasuresSequence[0]; + return pixelMeasures.PixelSpacing; +} + +function mapSlideCoord2PixelCoord(options) { + // X and Y Offset in Slide Coordinate System + if (!('offset' in options)) { + throw new Error('Option "offset" is required.'); + } + if (!Array.isArray(options.offset)) { + throw new Error('Option "offset" must be an array.'); + } + if (options.offset.length !== 2) { + throw new Error('Option "offset" must be an array with 2 elements.'); + } + const offset = options.offset; + + // Image Orientation Slide with direction cosines for Row and Column direction + if (!('orientation' in options)) { + throw new Error('Option "orientation" is required.'); + } + if (!Array.isArray(options.orientation)) { + throw new Error('Option "orientation" must be an array.'); + } + if (options.orientation.length !== 6) { + throw new Error('Option "orientation" must be an array with 6 elements.'); + } + const orientation = options.orientation; + + // Pixel Spacing along the Row and Column direction + if (!('spacing' in options)) { + throw new Error('Option "spacing" is required.'); + } + if (!Array.isArray(options.spacing)) { + throw new Error('Option "spacing" must be an array.'); + } + if (options.spacing.length !== 2) { + throw new Error('Option "spacing" must be an array with 2 elements.'); + } + const spacing = options.spacing; + + // X and Y coordinate in the Slide Coordinate System + if (!('point' in options)) { + throw new Error('Option "point" is required.'); + } + if (!Array.isArray(options.point)) { + throw new Error('Option "point" must be an array.'); + } + if (options.point.length !== 2) { + throw new Error('Option "point" must be an array with 2 elements.'); + } + const point = options.point; + + const m = [ + [orientation[0] * spacing[1], orientation[3] * spacing[0], offset[0]], + [orientation[1] * spacing[1], orientation[4] * spacing[0], offset[1]], + [0, 0, 1], + ]; + const mInverted = inv(m); + + const vSlide = [[point[0]], [point[1]], [1]]; + + const vImage = multiply(mInverted, vSlide); + + const row = Number(vImage[1][0].toFixed(4)); + const col = Number(vImage[0][0].toFixed(4)); + return [col, row]; +} diff --git a/extensions/dicom-microscopy/src/utils/dcmCodeValues.js b/extensions/dicom-microscopy/src/utils/dcmCodeValues.js new file mode 100644 index 000000000..82d489919 --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/dcmCodeValues.js @@ -0,0 +1,14 @@ +const DCM_CODE_VALUES = { + IMAGING_MEASUREMENTS: '126010', + MEASUREMENT_GROUP: '125007', + IMAGE_REGION: '111030', + FINDING: '121071', + TRACKING_UNIQUE_IDENTIFIER: '112039', + LENGTH: '410668003', + AREA: '42798000', + SHORT_AXIS: 'G-A186', + LONG_AXIS: 'G-A185', + ELLIPSE_AREA: 'G-D7FE', // TODO: Remove this +}; + +export default DCM_CODE_VALUES; diff --git a/extensions/dicom-microscopy/src/utils/dicomWebClient.ts b/extensions/dicom-microscopy/src/utils/dicomWebClient.ts new file mode 100644 index 000000000..8174d6c26 --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/dicomWebClient.ts @@ -0,0 +1,96 @@ +import { api } from 'dicomweb-client'; +import { errorHandler, DicomMetadataStore } from '@ohif/core'; + +/** + * create a DICOMwebClient object to be used by Dicom Microscopy Viewer + * + * Referenced the code from `/extensions/default/src/DicomWebDataSource/index.js` + * + * @param param0 + * @returns + */ +export default function getDicomWebClient({ + extensionManager, + servicesManager, +}) { + const dataSourceConfig = window.config.dataSources.find( + ds => ds.sourceName === extensionManager.activeDataSource + ); + const { userAuthenticationService } = servicesManager.services; + + const { wadoRoot, staticWado, singlepart } = dataSourceConfig.configuration; + + const wadoConfig = { + url: wadoRoot || '/dicomlocal', + staticWado, + singlepart, + headers: userAuthenticationService.getAuthorizationHeader(), + errorInterceptor: errorHandler.getHTTPErrorHandler(), + }; + + const client = new api.DICOMwebClient(wadoConfig); + client.wadoURL = wadoConfig.url; + + if (extensionManager.activeDataSource === 'dicomlocal') { + /** + * For local data source, override the retrieveInstanceFrames() method of the + * dicomweb-client to retrieve image data from memory cached metadata. + * Other methods of the client doesn't matter, as we are feeding the DMV + * with the series metadata already. + * + * @param {Object} options + * @param {String} options.studyInstanceUID - Study Instance UID + * @param {String} options.seriesInstanceUID - Series Instance UID + * @param {String} options.sopInstanceUID - SOP Instance UID + * @param {String} options.frameNumbers - One-based indices of Frame Items + * @param {Object} [options.queryParams] - HTTP query parameters + * @returns {ArrayBuffer[]} Rendered Frame Items as byte arrays + */ + // + client.retrieveInstanceFrames = async options => { + if (!('studyInstanceUID' in options)) { + throw new Error( + 'Study Instance UID is required for retrieval of instance frames' + ); + } + if (!('seriesInstanceUID' in options)) { + throw new Error( + 'Series Instance UID is required for retrieval of instance frames' + ); + } + if (!('sopInstanceUID' in options)) { + throw new Error( + 'SOP Instance UID is required for retrieval of instance frames' + ); + } + if (!('frameNumbers' in options)) { + throw new Error( + 'frame numbers are required for retrieval of instance frames' + ); + } + console.log( + `retrieve frames ${options.frameNumbers.toString()} of instance ${ + options.sopInstanceUID + }` + ); + + const instance = DicomMetadataStore.getInstance( + options.studyInstanceUID, + options.seriesInstanceUID, + options.sopInstanceUID + ); + + const frameNumbers = Array.isArray(options.frameNumbers) + ? options.frameNumbers + : options.frameNumbers.split(','); + + return frameNumbers.map(fr => + Array.isArray(instance.PixelData) + ? instance.PixelData[+fr - 1] + : instance.PixelData + ); + }; + } + + return client; +} diff --git a/extensions/dicom-microscopy/src/utils/getSourceDisplaySet.js b/extensions/dicom-microscopy/src/utils/getSourceDisplaySet.js new file mode 100644 index 000000000..d1455b639 --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/getSourceDisplaySet.js @@ -0,0 +1,38 @@ +/** + * Get referenced SM displaySet from SR displaySet + * + * @param {*} allDisplaySets + * @param {*} microscopySRDisplaySet + * @returns + */ +export default function getSourceDisplaySet( + allDisplaySets, + microscopySRDisplaySet +) { + const { ReferencedFrameOfReferenceUID } = microscopySRDisplaySet; + + const otherDisplaySets = allDisplaySets.filter( + ds => + ds.displaySetInstanceUID !== microscopySRDisplaySet.displaySetInstanceUID + ); + const referencedDisplaySet = otherDisplaySets.find( + displaySet => + displaySet.Modality === 'SM' && + (displaySet.FrameOfReferenceUID === ReferencedFrameOfReferenceUID || + // sometimes each depth instance has the different FrameOfReferenceID + displaySet.othersFrameOfReferenceUID.includes( + ReferencedFrameOfReferenceUID + )) + ); + + if (!referencedDisplaySet && otherDisplaySets.length >= 1) { + console.warn( + 'No display set with FrameOfReferenceUID', + ReferencedFrameOfReferenceUID, + 'single series, assuming data error, defaulting to only series.' + ); + return otherDisplaySets.find(displaySet => displaySet.Modality === 'SM'); + } + + return referencedDisplaySet; +} diff --git a/extensions/dicom-microscopy/src/utils/loadSR.js b/extensions/dicom-microscopy/src/utils/loadSR.js new file mode 100644 index 000000000..c690028bb --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/loadSR.js @@ -0,0 +1,207 @@ +import dcmjs from 'dcmjs'; + +import DCM_CODE_VALUES from './dcmCodeValues'; +import toArray from './toArray'; + +const MeasurementReport = + dcmjs.adapters.DICOMMicroscopyViewer.MeasurementReport; + +// Define as async so that it returns a promise, expected by the ViewportGrid +export default async function loadSR( + microscopyService, + microscopySRDisplaySet, + referencedDisplaySet +) { + const naturalizedDataset = microscopySRDisplaySet.metadata; + + const { StudyInstanceUID, FrameOfReferenceUID } = referencedDisplaySet; + + const managedViewers = microscopyService.getManagedViewersForStudy( + StudyInstanceUID + ); + + if (!managedViewers || !managedViewers.length) { + return; + } + + microscopySRDisplaySet.isLoaded = true; + + const { rois, labels } = await _getROIsFromToolState( + naturalizedDataset, + FrameOfReferenceUID + ); + + const managedViewer = managedViewers[0]; + + for (let i = 0; i < rois.length; i++) { + // NOTE: When saving Microscopy SR, we are attaching identifier property + // to each ROI, and when read for display, it is coming in as "TEXT" + // evaluation. + // As the Dicom Microscopy Viewer will override styles for "Text" evalutations + // to hide all other geometries, we are going to manually remove that + // evaluation item. + const roi = rois[i]; + const roiSymbols = Object.getOwnPropertySymbols(roi); + const _properties = roiSymbols.find(s => s.description === 'properties'); + const properties = roi[_properties]; + properties['evaluations'] = []; + + managedViewer.addRoiGraphicWithLabel(roi, labels[i]); + } +} + +async function _getROIsFromToolState(naturalizedDataset, FrameOfReferenceUID) { + const toolState = MeasurementReport.generateToolState(naturalizedDataset); + const tools = Object.getOwnPropertyNames(toolState); + + const DICOMMicroscopyViewer = await import( + /* webpackChunkName: "dicom-microscopy-viewer" */ 'dicom-microscopy-viewer' + ); + + const measurementGroupContentItems = _getMeasurementGroups( + naturalizedDataset + ); + + const rois = []; + const labels = []; + + tools.forEach(t => { + const toolSpecificToolState = toolState[t]; + let scoord3d; + + const capsToolType = t.toUpperCase(); + + const measurementGroupContentItemsForTool = measurementGroupContentItems.filter( + mg => { + const imageRegionContentItem = toArray(mg.ContentSequence).find( + ci => + ci.ConceptNameCodeSequence.CodeValue === + DCM_CODE_VALUES.IMAGE_REGION + ); + + return imageRegionContentItem.GraphicType === capsToolType; + } + ); + + toolSpecificToolState.forEach((coordinates, index) => { + const properties = {}; + + const options = { + coordinates, + frameOfReferenceUID: FrameOfReferenceUID, + }; + + if (t === 'Polygon') { + scoord3d = new DICOMMicroscopyViewer.scoord3d.Polygon(options); + } else if (t === 'Polyline') { + scoord3d = new DICOMMicroscopyViewer.scoord3d.Polyline(options); + } else if (t === 'Point') { + scoord3d = new DICOMMicroscopyViewer.scoord3d.Point(options); + } else if (t === 'Ellipse') { + scoord3d = new DICOMMicroscopyViewer.scoord3d.Ellipse(options); + } else { + throw new Error('Unsupported tool type'); + } + + const measurementGroup = measurementGroupContentItemsForTool[index]; + const findingGroup = toArray(measurementGroup.ContentSequence).find( + ci => ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.FINDING + ); + + const trackingGroup = toArray(measurementGroup.ContentSequence).find( + ci => + ci.ConceptNameCodeSequence.CodeValue === + DCM_CODE_VALUES.TRACKING_UNIQUE_IDENTIFIER + ); + + /** + * Extract presentation state from tracking identifier. + * Currently is stored in SR but should be stored in its tags. + */ + if (trackingGroup) { + const regExp = /\(([^)]+)\)/; + const matches = regExp.exec(trackingGroup.TextValue); + if (matches && matches[1]) { + properties.presentationState = JSON.parse(matches[1]); + properties.marker = properties.presentationState.marker; + } + } + + let measurements = toArray(measurementGroup.ContentSequence).filter(ci => + [ + DCM_CODE_VALUES.LENGTH, + DCM_CODE_VALUES.AREA, + DCM_CODE_VALUES.SHORT_AXIS, + DCM_CODE_VALUES.LONG_AXIS, + DCM_CODE_VALUES.ELLIPSE_AREA, + ].includes(ci.ConceptNameCodeSequence.CodeValue) + ); + + let evaluations = toArray(measurementGroup.ContentSequence).filter(ci => + [DCM_CODE_VALUES.TRACKING_UNIQUE_IDENTIFIER].includes( + ci.ConceptNameCodeSequence.CodeValue + ) + ); + + /** + * TODO: Resolve bug in DCMJS. + * ConceptNameCodeSequence should be a sequence with only one item. + */ + evaluations = evaluations.map(evaluation => { + const e = { ...evaluation }; + e.ConceptNameCodeSequence = toArray(e.ConceptNameCodeSequence); + return e; + }); + + /** + * TODO: Resolve bug in DCMJS. + * ConceptNameCodeSequence should be a sequence with only one item. + */ + measurements = measurements.map(measurement => { + const m = { ...measurement }; + m.ConceptNameCodeSequence = toArray(m.ConceptNameCodeSequence); + return m; + }); + + if (measurements && measurements.length) { + properties.measurements = measurements; + console.debug('[SR] retrieving measurements...', measurements); + } + + if (evaluations && evaluations.length) { + properties.evaluations = evaluations; + console.debug('[SR] retrieving evaluations...', evaluations); + } + + const roi = new DICOMMicroscopyViewer.roi.ROI({ scoord3d, properties }); + rois.push(roi); + + if (findingGroup) { + labels.push(findingGroup.ConceptCodeSequence.CodeValue); + } else { + labels.push(''); + } + }); + }); + + return { rois, labels }; +} + +function _getMeasurementGroups(naturalizedDataset) { + const { ContentSequence } = naturalizedDataset; + + const imagingMeasurementsContentItem = ContentSequence.find( + ci => + ci.ConceptNameCodeSequence.CodeValue === + DCM_CODE_VALUES.IMAGING_MEASUREMENTS + ); + + const measurementGroupContentItems = toArray( + imagingMeasurementsContentItem.ContentSequence + ).filter( + ci => + ci.ConceptNameCodeSequence.CodeValue === DCM_CODE_VALUES.MEASUREMENT_GROUP + ); + + return measurementGroupContentItems; +} diff --git a/extensions/dicom-microscopy/src/utils/saveByteArray.ts b/extensions/dicom-microscopy/src/utils/saveByteArray.ts new file mode 100644 index 000000000..d264fe7cd --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/saveByteArray.ts @@ -0,0 +1,12 @@ +/** + * Trigger file download from an array buffer + * @param buffer + * @param filename + */ +export function saveByteArray(buffer: ArrayBuffer, filename: string) { + var blob = new Blob([buffer], { type: 'application/dicom' }); + var link = document.createElement('a'); + link.href = window.URL.createObjectURL(blob); + link.download = filename; + link.click(); +} diff --git a/extensions/dicom-microscopy/src/utils/styles.js b/extensions/dicom-microscopy/src/utils/styles.js new file mode 100644 index 000000000..030b910bc --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/styles.js @@ -0,0 +1,48 @@ +const defaultFill = { + color: 'rgba(255,255,255,0.4)', +}; + +const emptyFill = { + color: 'rgba(255,255,255,0.0)', +}; + +const defaultStroke = { + color: 'rgb(0,255,0)', + width: 1.5, +}; + +const activeStroke = { + color: 'rgb(255,255,0)', + width: 1.5, +}; + +const defaultStyle = { + image: { + circle: { + fill: defaultFill, + stroke: activeStroke, + radius: 5, + }, + }, + fill: defaultFill, + stroke: activeStroke, +}; + +const emptyStyle = { + image: { + circle: { + fill: emptyFill, + stroke: defaultStroke, + radius: 5, + }, + }, + fill: emptyFill, + stroke: defaultStroke, +}; + +const styles = { + active: defaultStyle, + default: emptyStyle, +}; + +export default styles; diff --git a/extensions/dicom-microscopy/src/utils/toArray.js b/extensions/dicom-microscopy/src/utils/toArray.js new file mode 100644 index 000000000..2800085fa --- /dev/null +++ b/extensions/dicom-microscopy/src/utils/toArray.js @@ -0,0 +1,3 @@ +export default function toArray(item) { + return Array.isArray(item) ? item : [item]; +} diff --git a/extensions/dicom-microscopy/tsconfig.json b/extensions/dicom-microscopy/tsconfig.json new file mode 100644 index 000000000..e8977ec34 --- /dev/null +++ b/extensions/dicom-microscopy/tsconfig.json @@ -0,0 +1,11 @@ +{ + "compilerOptions": { + "outDir": "./dist/", + "noImplicitAny": true, + "module": "es6", + "target": "es5", + "jsx": "react", + "allowJs": true, + "moduleResolution": "node" + } +} diff --git a/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx b/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx index ec92ce6a3..e81309ce2 100644 --- a/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx +++ b/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx @@ -545,6 +545,7 @@ function _mapDisplaySets( const thumbnailNoImageModalities = [ 'SR', 'SEG', + 'SM', 'RTSTRUCT', 'RTPLAN', 'RTDOSE', diff --git a/modes/microscopy/.gitignore b/modes/microscopy/.gitignore new file mode 100644 index 000000000..67045665d --- /dev/null +++ b/modes/microscopy/.gitignore @@ -0,0 +1,104 @@ +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +lerna-debug.log* + +# Diagnostic reports (https://nodejs.org/api/report.html) +report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json + +# Runtime data +pids +*.pid +*.seed +*.pid.lock + +# Directory for instrumented libs generated by jscoverage/JSCover +lib-cov + +# Coverage directory used by tools like istanbul +coverage +*.lcov + +# nyc test coverage +.nyc_output + +# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files) +.grunt + +# Bower dependency directory (https://bower.io/) +bower_components + +# node-waf configuration +.lock-wscript + +# Compiled binary addons (https://nodejs.org/api/addons.html) +build/Release + +# Dependency directories +node_modules/ +jspm_packages/ + +# TypeScript v1 declaration files +typings/ + +# TypeScript cache +*.tsbuildinfo + +# Optional npm cache directory +.npm + +# Optional eslint cache +.eslintcache + +# Microbundle cache +.rpt2_cache/ +.rts2_cache_cjs/ +.rts2_cache_es/ +.rts2_cache_umd/ + +# Optional REPL history +.node_repl_history + +# Output of 'npm pack' +*.tgz + +# Yarn Integrity file +.yarn-integrity + +# dotenv environment variables file +.env +.env.test + +# parcel-bundler cache (https://parceljs.org/) +.cache + +# Next.js build output +.next + +# Nuxt.js build / generate output +.nuxt +dist + +# Gatsby files +.cache/ +# Comment in the public line in if your project uses Gatsby and *not* Next.js +# https://nextjs.org/blog/next-9-1#public-directory-support +# public + +# vuepress build output +.vuepress/dist + +# Serverless directories +.serverless/ + +# FuseBox cache +.fusebox/ + +# DynamoDB Local files +.dynamodb/ + +# TernJS port file +.tern-port diff --git a/modes/microscopy/.prettierrc b/modes/microscopy/.prettierrc new file mode 100644 index 000000000..b80ec6b34 --- /dev/null +++ b/modes/microscopy/.prettierrc @@ -0,0 +1,8 @@ +{ + "trailingComma": "es5", + "printWidth": 80, + "proseWrap": "always", + "tabWidth": 2, + "semi": true, + "singleQuote": true +} diff --git a/modes/microscopy/.webpack/webpack.dev.js b/modes/microscopy/.webpack/webpack.dev.js new file mode 100644 index 000000000..db7c206b1 --- /dev/null +++ b/modes/microscopy/.webpack/webpack.dev.js @@ -0,0 +1,8 @@ +const path = require('path'); +const webpackCommon = require('./../../../.webpack/webpack.base.js'); +const SRC_DIR = path.join(__dirname, '../src'); +const DIST_DIR = path.join(__dirname, '../dist'); + +module.exports = (env, argv) => { + return webpackCommon(env, argv, { SRC_DIR, DIST_DIR }); +}; diff --git a/modes/microscopy/.webpack/webpack.prod.js b/modes/microscopy/.webpack/webpack.prod.js new file mode 100644 index 000000000..163392a69 --- /dev/null +++ b/modes/microscopy/.webpack/webpack.prod.js @@ -0,0 +1,62 @@ +const path = require('path'); +const pkg = require('../package.json'); + +const outputFile = 'index.umd.js'; +const rootDir = path.resolve(__dirname, '../'); +const outputFolder = path.join(__dirname, `../dist/umd/${pkg.name}/`); + +// Todo: add ESM build for the mode in addition to umd build +const config = { + mode: 'production', + entry: rootDir + '/' + pkg.module, + devtool: 'source-map', + output: { + path: outputFolder, + filename: outputFile, + library: pkg.name, + libraryTarget: 'umd', + chunkFilename: '[name].chunk.js', + umdNamedDefine: true, + globalObject: "typeof self !== 'undefined' ? self : this", + }, + externals: [ + { + react: { + root: 'React', + commonjs2: 'react', + commonjs: 'react', + amd: 'react', + }, + '@ohif/core': { + commonjs2: '@ohif/core', + commonjs: '@ohif/core', + amd: '@ohif/core', + root: '@ohif/core', + }, + '@ohif/ui': { + commonjs2: '@ohif/ui', + commonjs: '@ohif/ui', + amd: '@ohif/ui', + root: '@ohif/ui', + }, + }, + ], + module: { + rules: [ + { + test: /(\.jsx|\.js|\.tsx|\.ts)$/, + loader: 'babel-loader', + exclude: /(node_modules|bower_components)/, + resolve: { + extensions: ['.js', '.jsx', '.ts', '.tsx'], + }, + }, + ], + }, + resolve: { + modules: [path.resolve('./node_modules'), path.resolve('./src')], + extensions: ['.json', '.js', '.jsx', '.tsx', '.ts'], + }, +}; + +module.exports = config; diff --git a/modes/microscopy/LICENSE b/modes/microscopy/LICENSE new file mode 100644 index 000000000..ccd0edc30 --- /dev/null +++ b/modes/microscopy/LICENSE @@ -0,0 +1,9 @@ +MIT License + +Copyright (c) 2023 microscopy (26860200+md-prog@users.noreply.github.com) + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. \ No newline at end of file diff --git a/modes/microscopy/README.md b/modes/microscopy/README.md new file mode 100644 index 000000000..e4bcca9d9 --- /dev/null +++ b/modes/microscopy/README.md @@ -0,0 +1,13 @@ +# OHIF mode for microscopy +Mode for *DICOM VL Whole Slide Microscopy Image*. +This mode uses [OHIF extension for microscopy](../../extensions/dicom-microscopy/). + + +## Acknowledgements + +- [DICOM Microscopy Viewer](https://github.com/ImagingDataCommons/dicom-microscopy-viewer) is a Vanilla JS library for web-based visualization of DICOM VL Whole Slide Microscopy Image datasets and derived information. +- [SLIM Viewer](https://github.com/imagingdatacommons/slim) is a single-page application for interactive visualization and annotation of digital whole slide microscopy images and derived image analysis results in standard DICOM format. The application is based on the dicom-microscopy-viewer JavaScript library and runs fully client side without any custom server components. + + +## License +MIT diff --git a/modes/microscopy/babel.config.js b/modes/microscopy/babel.config.js new file mode 100644 index 000000000..92fbbdeaf --- /dev/null +++ b/modes/microscopy/babel.config.js @@ -0,0 +1,44 @@ +module.exports = { + plugins: ['inline-react-svg', '@babel/plugin-proposal-class-properties'], + env: { + test: { + presets: [ + [ + // TODO: https://babeljs.io/blog/2019/03/19/7.4.0#migration-from-core-js-2 + '@babel/preset-env', + { + modules: 'commonjs', + debug: false, + }, + "@babel/preset-typescript", + ], + '@babel/preset-react', + ], + plugins: [ + '@babel/plugin-proposal-object-rest-spread', + '@babel/plugin-syntax-dynamic-import', + '@babel/plugin-transform-regenerator', + '@babel/plugin-transform-runtime', + ], + }, + production: { + presets: [ + // WebPack handles ES6 --> Target Syntax + ['@babel/preset-env', { modules: false }], + '@babel/preset-react', + "@babel/preset-typescript", + ], + ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'], + }, + development: { + presets: [ + // WebPack handles ES6 --> Target Syntax + ['@babel/preset-env', { modules: false }], + '@babel/preset-react', + "@babel/preset-typescript", + ], + plugins: ['react-hot-loader/babel'], + ignore: ['**/*.test.jsx', '**/*.test.js', '__snapshots__', '__tests__'], + }, + }, +}; diff --git a/modes/microscopy/package.json b/modes/microscopy/package.json new file mode 100644 index 000000000..8a8443e42 --- /dev/null +++ b/modes/microscopy/package.json @@ -0,0 +1,65 @@ +{ + "name": "@ohif/mode-microscopy", + "version": "3.0.0", + "description": "OHIF mode for DICOM microscopy", + "author": "Bill Wallace, md-prog", + "license": "MIT", + "main": "dist/umd/@ohif/mode-microscopy/index.umd.js", + "files": [ + "dist/**", + "public/**", + "README.md" + ], + "repository": "OHIF/Viewers", + "keywords": [ + "ohif-mode" + ], + "module": "src/index.tsx", + "engines": { + "node": ">=14", + "npm": ">=6", + "yarn": ">=1.16.0" + }, + "scripts": { + "dev": "cross-env NODE_ENV=development webpack --config .webpack/webpack.dev.js --watch --debug --output-pathinfo", + "dev:cornerstone": "yarn run dev", + "build": "cross-env NODE_ENV=production webpack --config .webpack/webpack.prod.js", + "build:package": "yarn run build", + "start": "yarn run dev", + "test:unit": "jest --watchAll", + "test:unit:ci": "jest --ci --runInBand --collectCoverage --passWithNoTests" + }, + "peerDependencies": { + "@ohif/core": "^3.0.0", + "@ohif/extension-dicom-microscopy": "^3.0.0" + }, + "dependencies": { + "@babel/runtime": "^7.20.13" + }, + "devDependencies": { + "@babel/core": "^7.17.8", + "@babel/plugin-proposal-class-properties": "^7.16.7", + "@babel/plugin-proposal-object-rest-spread": "^7.17.3", + "@babel/plugin-proposal-private-methods": "^7.18.6", + "@babel/plugin-syntax-dynamic-import": "^7.8.3", + "@babel/plugin-transform-arrow-functions": "^7.16.7", + "@babel/plugin-transform-regenerator": "^7.16.7", + "@babel/plugin-transform-runtime": "^7.17.0", + "@babel/plugin-transform-typescript": "^7.13.0", + "@babel/preset-env": "^7.16.11", + "@babel/preset-react": "^7.16.7", + "@babel/preset-typescript": "^7.13.0", + "babel-eslint": "^8.0.3", + "babel-loader": "^8.0.0-beta.4", + "babel-plugin-inline-react-svg": "^2.0.1", + "clean-webpack-plugin": "^4.0.0", + "copy-webpack-plugin": "^10.2.0", + "cross-env": "^7.0.3", + "dotenv": "^14.1.0", + "eslint": "^5.0.1", + "eslint-loader": "^2.0.0", + "webpack": "^5.50.0", + "webpack-merge": "^5.7.3", + "webpack-cli": "^4.7.2" + } +} diff --git a/modes/microscopy/src/id.js b/modes/microscopy/src/id.js new file mode 100644 index 000000000..ebe5acd98 --- /dev/null +++ b/modes/microscopy/src/id.js @@ -0,0 +1,5 @@ +import packageJson from '../package.json'; + +const id = packageJson.name; + +export { id }; diff --git a/modes/microscopy/src/index.tsx b/modes/microscopy/src/index.tsx new file mode 100644 index 000000000..9044ad6eb --- /dev/null +++ b/modes/microscopy/src/index.tsx @@ -0,0 +1,142 @@ +import { hotkeys } from '@ohif/core'; + +import { id } from './id'; +import toolbarButtons from './toolbarButtons'; + +const ohif = { + layout: '@ohif/extension-default.layoutTemplateModule.viewerLayout', + sopClassHandler: '@ohif/extension-default.sopClassHandlerModule.stack', + hangingProtocols: '@ohif/extension-default.hangingProtocolModule.default', + leftPanel: '@ohif/extension-default.panelModule.seriesList', + rightPanel: '@ohif/extension-default.panelModule.measure', +}; + +export const cornerstone = { + viewport: '@ohif/extension-cornerstone.viewportModule.cornerstone', +}; + +const dicomvideo = { + sopClassHandler: + '@ohif/extension-dicom-video.sopClassHandlerModule.dicom-video', + viewport: '@ohif/extension-dicom-video.viewportModule.dicom-video', +}; + +const dicompdf = { + sopClassHandler: '@ohif/extension-dicom-pdf.sopClassHandlerModule.dicom-pdf', + viewport: '@ohif/extension-dicom-pdf.viewportModule.dicom-pdf', +}; + +const extensionDependencies = { + // Can derive the versions at least process.env.from npm_package_version + '@ohif/extension-default': '^3.0.0', + '@ohif/extension-cornerstone': '^3.0.0', + '@ohif/extension-cornerstone-dicom-sr': '^3.0.0', + '@ohif/extension-dicom-pdf': '^3.0.1', + '@ohif/extension-dicom-video': '^3.0.1', + '@ohif/extension-dicom-microscopy': '^3.0.0', +}; + +function modeFactory() { + return { + // TODO: We're using this as a route segment + // We should not be. + id, + routeName: 'microscopy', + displayName: 'Microscopy', + + /** + * Lifecycle hooks + */ + onModeEnter: ({ servicesManager, extensionManager, commandsManager }) => { + const { toolbarService } = servicesManager.services; + + toolbarService.init(extensionManager); + toolbarService.addButtons(toolbarButtons); + toolbarService.createButtonSection('primary', [ + 'MeasurementTools', + 'dragPan', + ]); + }, + + onModeExit: ({ servicesManager }) => { + const { toolbarService } = servicesManager.services; + + toolbarService.reset(); + }, + + validationTags: { + study: [], + series: [], + }, + + isValidMode: ({ modalities }) => { + const modalities_list = modalities.split('\\'); + + // Slide Microscopy and ECG modality not supported by basic mode yet + return modalities_list.includes('SM'); + }, + + routes: [ + { + path: 'microscopy', + /*init: ({ servicesManager, extensionManager }) => { + //defaultViewerRouteInit + },*/ + layoutTemplate: ({ location, servicesManager }) => { + return { + id: ohif.layout, + props: { + leftPanels: [ohif.leftPanel], + leftPanelDefaultClosed: true, // we have problem with rendering thumbnails for microscopy images + rightPanelDefaultClosed: true, // we do not have the save microscopy measurements yet + rightPanels: [ + '@ohif/extension-dicom-microscopy.panelModule.measure', + ], + viewports: [ + { + namespace: + '@ohif/extension-dicom-microscopy.viewportModule.microscopy-dicom', + displaySetsToDisplay: [ + '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySopClassHandler', + '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySRSopClassHandler', + ], + }, + { + namespace: dicomvideo.viewport, + displaySetsToDisplay: [dicomvideo.sopClassHandler], + }, + { + namespace: dicompdf.viewport, + displaySetsToDisplay: [dicompdf.sopClassHandler], + }, + ], + }, + }; + }, + }, + ], + extensions: extensionDependencies, + hangingProtocols: [ohif.hangingProtocols], + hangingProtocol: ['default'], + + // Order is important in sop class handlers when two handlers both use + // the same sop class under different situations. In that case, the more + // general handler needs to come last. For this case, the dicomvideo must + // come first to remove video transfer syntax before ohif uses images + sopClassHandlers: [ + '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySopClassHandler', + '@ohif/extension-dicom-microscopy.sopClassHandlerModule.DicomMicroscopySRSopClassHandler', + dicomvideo.sopClassHandler, + dicompdf.sopClassHandler, + ], + hotkeys: [...hotkeys.defaults.hotkeyBindings], + }; +} + +const mode = { + id, + modeFactory, + extensionDependencies, +}; + +export default mode; diff --git a/modes/microscopy/src/toolbarButtons.js b/modes/microscopy/src/toolbarButtons.js new file mode 100644 index 000000000..40078c5de --- /dev/null +++ b/modes/microscopy/src/toolbarButtons.js @@ -0,0 +1,184 @@ +// TODO: torn, can either bake this here; or have to create a whole new button type +/** + * + * @param {*} type - 'tool' | 'action' | 'toggle' + * @param {*} id + * @param {*} icon + * @param {*} label + */ +function _createButton(type, id, icon, label, commands, tooltip) { + return { + id, + icon, + label, + type, + commands, + tooltip, + }; +} + +const _createActionButton = _createButton.bind(null, 'action'); +const _createToggleButton = _createButton.bind(null, 'toggle'); +const _createToolButton = _createButton.bind(null, 'tool'); + +const toolbarButtons = [ + // Measurement + { + id: 'MeasurementTools', + type: 'ohif.splitButton', + props: { + groupId: 'MeasurementTools', + isRadio: true, // ? + // Switch? + primary: _createToolButton( + 'line', + 'tool-length', + 'Line', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'line', + }, + context: 'MICROSCOPY', + }, + ], + 'Line' + ), + secondary: { + icon: 'chevron-down', + label: '', + isActive: true, + tooltip: 'More Measure Tools', + }, + items: [ + _createToolButton( + 'line', + 'tool-length', + 'Line', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'line', + }, + context: 'MICROSCOPY', + }, + ], + 'Line Tool' + ), + _createToolButton( + 'point', + 'tool-point', + 'Point', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'point', + }, + context: 'MICROSCOPY', + }, + ], + 'Point Tool' + ), + _createToolButton( + 'polygon', + 'tool-polygon', + 'Polygon', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'polygon', + }, + context: 'MICROSCOPY', + }, + ], + 'Polygon Tool' + ), + _createToolButton( + 'circle', + 'tool-circle', + 'Circle', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'circle', + }, + context: 'MICROSCOPY', + }, + ], + 'Circle Tool' + ), + _createToolButton( + 'box', + 'tool-rectangle', + 'Box', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'box', + }, + context: 'MICROSCOPY', + }, + ], + 'Box Tool' + ), + _createToolButton( + 'freehandpolygon', + 'tool-freehand-polygon', + 'Freehand Polygon', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'freehandpolygon', + }, + context: 'MICROSCOPY', + }, + ], + 'Freehand Polygon Tool' + ), + _createToolButton( + 'freehandline', + 'tool-freehand-line', + 'Freehand Line', + [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'freehandline', + }, + context: 'MICROSCOPY', + }, + ], + 'Freehand Line Tool' + ), + ], + }, + }, + // Pan... + { + id: 'dragPan', + type: 'ohif.radioGroup', + props: { + type: 'tool', + icon: 'tool-move', + label: 'Pan', + commands: [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'dragPan', + }, + context: 'MICROSCOPY', + }, + ], + }, + }, +]; + +export default toolbarButtons; diff --git a/platform/core/src/services/DicomMetadataStore/createStudyMetadata.js b/platform/core/src/services/DicomMetadataStore/createStudyMetadata.js index 4822b616c..dc43aa503 100644 --- a/platform/core/src/services/DicomMetadataStore/createStudyMetadata.js +++ b/platform/core/src/services/DicomMetadataStore/createStudyMetadata.js @@ -27,7 +27,7 @@ function createStudyMetadata(StudyInstanceUID) { const series = createSeriesMetadata([instance]); this.series.push(series); const { Modality } = series; - if (this.ModalitiesInStudy.indexof(Modality) === -1) { + if (this.ModalitiesInStudy.indexOf(Modality) === -1) { this.ModalitiesInStudy.push(Modality); } } diff --git a/platform/core/src/utils/isLowPriorityModality.ts b/platform/core/src/utils/isLowPriorityModality.ts index 54024d5a0..aebb450ff 100644 --- a/platform/core/src/utils/isLowPriorityModality.ts +++ b/platform/core/src/utils/isLowPriorityModality.ts @@ -1,4 +1,10 @@ -const LOW_PRIORITY_MODALITIES = Object.freeze(['SEG', 'KO', 'PR', 'SR', 'RTSTRUCT']); +const LOW_PRIORITY_MODALITIES = Object.freeze([ + 'SEG', + 'KO', + 'PR', + 'SR', + 'RTSTRUCT', +]); export default function isLowPriorityModality(Modality) { return LOW_PRIORITY_MODALITIES.includes(Modality); diff --git a/platform/ui/src/assets/icons/tool-freehand-polygon.svg b/platform/ui/src/assets/icons/tool-freehand-polygon.svg new file mode 100644 index 000000000..bfc1b0dcd --- /dev/null +++ b/platform/ui/src/assets/icons/tool-freehand-polygon.svg @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/platform/ui/src/assets/icons/tool-freehand.svg b/platform/ui/src/assets/icons/tool-freehand.svg new file mode 100644 index 000000000..2159f9150 --- /dev/null +++ b/platform/ui/src/assets/icons/tool-freehand.svg @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/platform/ui/src/assets/icons/tool-polygon.svg b/platform/ui/src/assets/icons/tool-polygon.svg new file mode 100644 index 000000000..ff2f9e029 --- /dev/null +++ b/platform/ui/src/assets/icons/tool-polygon.svg @@ -0,0 +1,3 @@ + + + diff --git a/platform/ui/src/components/Icon/getIcon.js b/platform/ui/src/components/Icon/getIcon.js index b8df5463d..3627697af 100644 --- a/platform/ui/src/components/Icon/getIcon.js +++ b/platform/ui/src/components/Icon/getIcon.js @@ -97,6 +97,9 @@ import toolRectangle from './../../assets/icons/tool-rectangle.svg'; import toolFusionColor from './../../assets/icons/tool-fusion-color.svg'; import toolCreateThreshold from './../../assets/icons/tool-create-threshold.svg'; import toolCalibration from './../../assets/icons/tool-calibration.svg'; +import toolFreehand from './../../assets/icons/tool-freehand.svg'; +import toolFreehandPolygon from './../../assets/icons/tool-freehand-polygon.svg'; +import toolPolygon from './../../assets/icons/tool-polygon.svg'; import editPatient from './../../assets/icons/edit-patient.svg'; import panelGroupMore from './../../assets/icons/panel-group-more.svg'; import panelGroupOpenClose from './../../assets/icons/panel-group-open-close.svg'; @@ -216,6 +219,11 @@ const ICONS = { 'tool-fusion-color': toolFusionColor, 'tool-create-threshold': toolCreateThreshold, 'tool-calibration': toolCalibration, + 'tool-point': toolCircle, + 'tool-circle': toolCircle, + 'tool-freehand-line': toolFreehand, + 'tool-freehand-polygon': toolFreehandPolygon, + 'tool-polygon': toolPolygon, 'edit-patient': editPatient, 'icon-mpr': iconMPR, 'icon-next-inactive': iconNextInactive, diff --git a/platform/viewer/.webpack/webpack.pwa.js b/platform/viewer/.webpack/webpack.pwa.js index 904f3503b..fa403148c 100644 --- a/platform/viewer/.webpack/webpack.pwa.js +++ b/platform/viewer/.webpack/webpack.pwa.js @@ -10,7 +10,6 @@ const CopyWebpackPlugin = require('copy-webpack-plugin'); const HtmlWebpackPlugin = require('html-webpack-plugin'); const { InjectManifest } = require('workbox-webpack-plugin'); const MiniCssExtractPlugin = require('mini-css-extract-plugin'); -const CopyPlugin = require('copy-webpack-plugin'); // ~~ Directories const SRC_DIR = path.join(__dirname, '../src'); const DIST_DIR = path.join(__dirname, '../dist'); @@ -101,6 +100,21 @@ module.exports = (env, argv) => { from: `${PUBLIC_DIR}/${APP_CONFIG}`, to: `${DIST_DIR}/app-config.js`, }, + // Copy Dicom Microscopy Viewer build files + { + from: + '../../../node_modules/dicom-microscopy-viewer/dist/dynamic-import', + to: DIST_DIR, + globOptions: { + ignore: ['*.js.map'], + }, + }, + // Copy dicom-image-loader build files + { + from: + '../../../node_modules/@cornerstonejs/dicom-image-loader/dist/dynamic-import', + to: DIST_DIR, + }, ], }), // Generate "index.html" w/ correct includes/imports @@ -120,15 +134,6 @@ module.exports = (env, argv) => { // Need to exclude the theme as it is updated independently exclude: [/theme/], }), - new CopyPlugin({ - patterns: [ - { - from: - '../../../node_modules/@cornerstonejs/dicom-image-loader/dist/dynamic-import', - to: DIST_DIR, - }, - ], - }), ], // https://webpack.js.org/configuration/dev-server/ devServer: { diff --git a/platform/viewer/package.json b/platform/viewer/package.json index e8a7bceb8..94c7463eb 100644 --- a/platform/viewer/package.json +++ b/platform/viewer/package.json @@ -55,11 +55,13 @@ "@ohif/extension-default": "^3.0.0", "@ohif/extension-dicom-pdf": "^3.0.1", "@ohif/extension-dicom-video": "^3.0.1", + "@ohif/extension-dicom-microscopy": "^3.0.0", "@ohif/extension-test": "0.0.1", "@ohif/i18n": "^1.0.0", "@ohif/mode-basic-dev-mode": "^3.0.0", "@ohif/mode-test": "^0.0.1", "@ohif/mode-longitudinal": "^3.0.0", + "@ohif/mode-microscopy": "^3.0.0", "@ohif/ui": "^2.0.0", "@types/react": "^17.0.38", "classnames": "^2.3.2", diff --git a/platform/viewer/pluginConfig.json b/platform/viewer/pluginConfig.json index 8c5d24197..37e90e765 100644 --- a/platform/viewer/pluginConfig.json +++ b/platform/viewer/pluginConfig.json @@ -16,6 +16,10 @@ "packageName": "@ohif/extension-default", "version": "3.0.0" }, + { + "packageName": "@ohif/extension-dicom-microscopy", + "version": "3.0.0" + }, { "packageName": "@ohif/extension-dicom-pdf", "version": "3.0.1" @@ -42,6 +46,10 @@ "packageName": "@ohif/mode-longitudinal", "version": "3.0.0" }, + { + "packageName": "@ohif/mode-microscopy", + "version": "3.0.0" + }, { "packageName": "@ohif/mode-tmtv", "version": "3.0.0" diff --git a/platform/viewer/public/config/demo.js b/platform/viewer/public/config/demo.js index 433d56845..c9e17261d 100644 --- a/platform/viewer/public/config/demo.js +++ b/platform/viewer/public/config/demo.js @@ -1,5 +1,6 @@ window.config = { routerBasename: '/', + modes: [], extensions: [], showStudyList: true, // below flag is for performance reasons, but it might not work for all servers @@ -7,21 +8,24 @@ window.config = { showWarningMessageForCrossOrigin: true, strictZSpacingForVolumeViewport: true, showCPUFallbackMessage: true, - servers: { - dicomWeb: [ - { + dataSources: [ + { + friendlyName: 'DCM4CHEE Server', + namespace: '@ohif/extension-default.dataSourcesModule.dicomweb', + sourceName: 'dicomweb', + configuration: { name: 'DCM4CHEE', wadoUriRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb', qidoRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb', wadoRoot: 'https://domvja9iplmyu.cloudfront.net/dicomweb', qidoSupportsIncludeField: true, imageRendering: 'wadors', - thumbnailRendering: 'wadors', enableStudyLazyLoad: true, useBulkDataURI: false, }, - ], - }, + }, + ], + defaultDataSourceName: 'dicomweb', hotkeys: [ { commandName: 'incrementActiveViewport', diff --git a/platform/viewer/src/routes/Local/Local.tsx b/platform/viewer/src/routes/Local/Local.tsx index af0dea070..ddd0834e3 100644 --- a/platform/viewer/src/routes/Local/Local.tsx +++ b/platform/viewer/src/routes/Local/Local.tsx @@ -1,7 +1,7 @@ import React, { useEffect, useRef } from 'react'; import classnames from 'classnames'; import { useNavigate } from 'react-router-dom'; -import { MODULE_TYPES } from '@ohif/core'; +import { DicomMetadataStore, MODULE_TYPES } from '@ohif/core'; import Dropzone from 'react-dropzone'; import filesToStudies from './filesToStudies'; @@ -60,12 +60,41 @@ function Local() { const firstLocalDataSource = localDataSources[0]; const dataSource = firstLocalDataSource.createDataSource({}); + const microscopyExtensionLoaded = extensionManager.registeredExtensionIds.includes( + '@ohif/extension-dicom-microscopy' + ); + + let modePath = 'viewer'; + const onDrop = async acceptedFiles => { const studies = await filesToStudies(acceptedFiles, dataSource); - // Todo: navigate to work list and let user select a mode + const query = new URLSearchParams(); + + if (microscopyExtensionLoaded) { + // TODO: for microscopy, we are forcing microscopy mode, which is not ideal. + // we should make the local drag and drop navigate to the worklist and + // there user can select microscopy mode + const smStudies = studies.filter(id => { + const study = DicomMetadataStore.getStudy(id); + return ( + study.series.findIndex( + s => s.Modality === 'SM' || s.instances[0].Modality === 'SM' + ) >= 0 + ); + }); + + if (smStudies.length > 0) { + smStudies.forEach(id => query.append('StudyInstanceUIDs', id)); + + modePath = 'microscopy'; + } + } + + // Todo: navigate to work list and let user select a mode studies.forEach(id => query.append('StudyInstanceUIDs', id)); - navigate(`/viewer/dicomlocal?${decodeURIComponent(query.toString())}`); + + navigate(`/${modePath}/dicomlocal?${decodeURIComponent(query.toString())}`); }; // Set body style diff --git a/yarn.lock b/yarn.lock index 0cf65bf1f..e4f3f7807 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1272,7 +1272,7 @@ core-js-pure "^3.25.1" regenerator-runtime "^0.13.11" -"@babel/runtime@7.17.9", "@babel/runtime@7.7.6", "@babel/runtime@^7.1.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.14.6", "@babel/runtime@^7.17.8", "@babel/runtime@^7.18.6", "@babel/runtime@^7.20.13", "@babel/runtime@^7.20.7", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.2", "@babel/runtime@^7.7.4", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.9.2": +"@babel/runtime@7.17.9", "@babel/runtime@7.7.6", 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"https://registry.yarnpkg.com/resolve-protobuf-schema/-/resolve-protobuf-schema-2.1.0.tgz#9ca9a9e69cf192bbdaf1006ec1973948aa4a3758" + integrity sha512-kI5ffTiZWmJaS/huM8wZfEMer1eRd7oJQhDuxeCLe3t7N7mX3z94CN0xPxBQxFYQTSNz9T0i+v6inKqSdK8xrQ== + dependencies: + protocol-buffers-schema "^3.3.1" + resolve-url@^0.2.1: version "0.2.1" resolved "https://registry.npmjs.org/resolve-url/-/resolve-url-0.2.1.tgz#2c637fe77c893afd2a663fe21aa9080068e2052a" @@ -19219,6 +19459,11 @@ run-queue@^1.0.0, run-queue@^1.0.3: dependencies: aproba "^1.1.1" +rw@^1.3.3: + version "1.3.3" + resolved "https://registry.yarnpkg.com/rw/-/rw-1.3.3.tgz#3f862dfa91ab766b14885ef4d01124bfda074fb4" + integrity sha512-PdhdWy89SiZogBLaw42zdeqtRJ//zFd2PgQavcICDUgJT5oW10QCRKbJ6bg4r0/UY2M6BWd5tkxuGFRvCkgfHQ== + rxjs@^6.3.3, rxjs@^6.4.0: version "6.6.7" resolved "https://registry.npmjs.org/rxjs/-/rxjs-6.6.7.tgz#90ac018acabf491bf65044235d5863c4dab804c9" @@ -19368,7 +19613,7 @@ section-matter@^1.0.0: extend-shallow "^2.0.1" kind-of "^6.0.0" -seedrandom@3.0.5: +seedrandom@3.0.5, seedrandom@^3.0.5: version "3.0.5" resolved "https://registry.npmjs.org/seedrandom/-/seedrandom-3.0.5.tgz#54edc85c95222525b0c7a6f6b3543d8e0b3aa0a7" integrity sha512-8OwmbklUNzwezjGInmZ+2clQmExQPvomqjL7LFqOYqtmuxRgQYqOD3mHaU+MvZn5FLUeVxVfQjwLZW/n/JFuqg== @@ -19813,11 +20058,21 @@ socks@~2.3.2: ip "1.1.5" smart-buffer "^4.1.0" +sort-asc@^0.1.0: + version "0.1.0" + resolved "https://registry.yarnpkg.com/sort-asc/-/sort-asc-0.1.0.tgz#ab799df61fc73ea0956c79c4b531ed1e9e7727e9" + integrity sha512-jBgdDd+rQ+HkZF2/OHCmace5dvpos/aWQpcxuyRs9QUbPRnkEJmYVo81PIGpjIdpOcsnJ4rGjStfDHsbn+UVyw== + sort-css-media-queries@2.1.0: version "2.1.0" resolved "https://registry.npmjs.org/sort-css-media-queries/-/sort-css-media-queries-2.1.0.tgz#7c85e06f79826baabb232f5560e9745d7a78c4ce" integrity sha512-IeWvo8NkNiY2vVYdPa27MCQiR0MN0M80johAYFVxWWXQ44KU84WNxjslwBHmc/7ZL2ccwkM7/e6S5aiKZXm7jA== +sort-desc@^0.1.1: + version "0.1.1" + resolved "https://registry.yarnpkg.com/sort-desc/-/sort-desc-0.1.1.tgz#198b8c0cdeb095c463341861e3925d4ee359a9ee" + integrity sha512-jfZacW5SKOP97BF5rX5kQfJmRVZP5/adDUTY8fCSPvNcXDVpUEe2pr/iKGlcyZzchRJZrswnp68fgk3qBXgkJw== + sort-keys@^1.0.0: version "1.1.2" resolved "https://registry.npmjs.org/sort-keys/-/sort-keys-1.1.2.tgz#441b6d4d346798f1b4e49e8920adfba0e543f9ad" @@ -19832,6 +20087,14 @@ sort-keys@^2.0.0: dependencies: is-plain-obj "^1.0.0" +sort-object@^0.3.2: + version "0.3.2" + resolved "https://registry.yarnpkg.com/sort-object/-/sort-object-0.3.2.tgz#98e0d199ede40e07c61a84403c61d6c3b290f9e2" + integrity sha512-aAQiEdqFTTdsvUFxXm3umdo04J7MRljoVGbBlkH7BgNsMvVNAJyGj7C/wV1A8wHWAJj/YikeZbfuCKqhggNWGA== + dependencies: + sort-asc "^0.1.0" + sort-desc "^0.1.1" + source-list-map@^2.0.0: version "2.0.1" resolved "https://registry.npmjs.org/source-list-map/-/source-list-map-2.0.1.tgz#3993bd873bfc48479cca9ea3a547835c7c154b34" @@ -20823,6 +21086,11 @@ timsort@^0.3.0: resolved "https://registry.npmjs.org/timsort/-/timsort-0.3.0.tgz#405411a8e7e6339fe64db9a234de11dc31e02bd4" integrity sha512-qsdtZH+vMoCARQtyod4imc2nIJwg9Cc7lPRrw9CzF8ZKR0khdr8+2nX80PBhET3tcyTtJDxAffGh2rXH4tyU8A== +tiny-emitter@^2.1.0: + version "2.1.0" + resolved "https://registry.yarnpkg.com/tiny-emitter/-/tiny-emitter-2.1.0.tgz#1d1a56edfc51c43e863cbb5382a72330e3555423" + integrity sha512-NB6Dk1A9xgQPMoGqC5CVXn123gWyte215ONT5Pp5a0yt4nlEoO1ZWeCwpncaekPHXO60i47ihFnZPiRPjRMq4Q== + tiny-invariant@^1.0.2: version "1.3.1" resolved "https://registry.npmjs.org/tiny-invariant/-/tiny-invariant-1.3.1.tgz#8560808c916ef02ecfd55e66090df23a4b7aa642" @@ -21084,6 +21352,11 @@ typed-array-length@^1.0.4: for-each "^0.3.3" is-typed-array "^1.1.9" +typed-function@^4.1.0: + version "4.1.0" + resolved "https://registry.npmjs.org/typed-function/-/typed-function-4.1.0.tgz#da4bdd8a6d19a89e22732f75e4a410860aaf9712" + integrity sha512-DGwUl6cioBW5gw2L+6SMupGwH/kZOqivy17E4nsh1JI9fKF87orMmlQx3KISQPmg3sfnOUGlwVkroosvgddrlg== + typedarray-to-buffer@^3.1.5: version "3.1.5" resolved "https://registry.npmjs.org/typedarray-to-buffer/-/typedarray-to-buffer-3.1.5.tgz#a97ee7a9ff42691b9f783ff1bc5112fe3fca9080" @@ -21580,7 +21853,7 @@ uuid@^8.3.2: resolved "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz#80d5b5ced271bb9af6c445f21a1a04c606cefbe2" integrity sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg== -uuid@^9.0.0: +uuid@^9.0, uuid@^9.0.0: version "9.0.0" resolved "https://registry.npmjs.org/uuid/-/uuid-9.0.0.tgz#592f550650024a38ceb0c562f2f6aa435761efb5" integrity sha512-MXcSTerfPa4uqyzStbRoTgt5XIe3x5+42+q1sDuy3R5MDk66URdLMOZe5aPX/SQd+kuYAh0FdP/pO28IkQyTeg== @@ -21779,6 +22052,11 @@ web-streams-polyfill@^3.0.3: resolved "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.2.1.tgz#71c2718c52b45fd49dbeee88634b3a60ceab42a6" integrity sha512-e0MO3wdXWKrLbL0DgGnUV7WHVuw9OUvL4hjgnPkIeEvESk74gAITi5G606JtZPp39cd8HA9VQzCIvA49LpPN5Q== +web-worker@^1.2.0: + version "1.2.0" + resolved "https://registry.yarnpkg.com/web-worker/-/web-worker-1.2.0.tgz#5d85a04a7fbc1e7db58f66595d7a3ac7c9c180da" + integrity sha512-PgF341avzqyx60neE9DD+XS26MMNMoUQRz9NOZwW32nPQrF6p77f1htcnjBSEV8BGMKZ16choqUG4hyI0Hx7mA== + webgl-constants@^1.1.1: version "1.1.1" resolved "https://registry.npmjs.org/webgl-constants/-/webgl-constants-1.1.1.tgz#f9633ee87fea56647a60b9ce735cbdfb891c6855" @@ -22499,6 +22777,11 @@ xml-name-validator@^3.0.0: resolved "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-3.0.0.tgz#6ae73e06de4d8c6e47f9fb181f78d648ad457c6a" integrity sha512-A5CUptxDsvxKJEU3yO6DuWBSJz/qizqzJKOMIfUJHETbBw/sFaDxgd6fxm1ewUaM0jZ444Fc5vC5ROYurg/4Pw== +xml-utils@^1.0.2: + version "1.3.0" + resolved "https://registry.yarnpkg.com/xml-utils/-/xml-utils-1.3.0.tgz#f1043534e3ac3deda12ddab39f8442e16da98ebb" + integrity sha512-i4PIrX33Wd66dvwo4syicwlwmnr6wuvvn4f2ku9hA67C2Uk62Xubczuhct+Evnd12/DV71qKNeDdJwES8HX1RA== + xml@^1.0.1: version "1.0.1" resolved "https://registry.npmjs.org/xml/-/xml-1.0.1.tgz#78ba72020029c5bc87b8a81a3cfcd74b4a2fc1e5" From fe7fa6e5bf2db1019e5ce42dbff06146e4139a7b Mon Sep 17 00:00:00 2001 From: Braden Morley <63816946+bradenjmorley@users.noreply.github.com> Date: Fri, 28 Apr 2023 01:01:53 +0000 Subject: [PATCH 19/54] fix(ui): updated input fields to match new color scheme (#3323) * Updated input fields to match new color scheme Added small input text fields and fixed coloring * Added tailwind changes to viewers file --- platform/ui/src/components/Input/Input.tsx | 10 +++++++++- .../components/Input/__stories__/input.stories.mdx | 13 +++++++++++++ .../ui/src/components/InputNumber/InputNumber.css | 6 +++++- .../ui/src/components/InputNumber/InputNumber.tsx | 7 +++---- platform/ui/src/components/InputText/InputText.tsx | 4 ++-- platform/ui/tailwind.config.js | 7 +++++++ platform/viewer/tailwind.config.js | 7 +++++++ 7 files changed, 46 insertions(+), 8 deletions(-) diff --git a/platform/ui/src/components/Input/Input.tsx b/platform/ui/src/components/Input/Input.tsx index a03a4ae7e..2940348b8 100644 --- a/platform/ui/src/components/Input/Input.tsx +++ b/platform/ui/src/components/Input/Input.tsx @@ -4,13 +4,18 @@ import Label from '../Label'; import classnames from 'classnames'; const baseInputClasses = - 'shadow transition duration-300 appearance-none border border-primary-main hover:border-gray-500 focus:border-gray-500 focus:outline-none rounded w-full py-2 px-3 text-sm text-white leading-tight focus:outline-none'; + 'shadow transition duration-300 appearance-none border border-inputfield-main focus:border-inputfield-focus focus:outline-none disabled:border-inputfield-disabled rounded w-full py-2 px-3 text-sm text-white placeholder-inputfield-placeholder leading-tight'; const transparentClasses = { true: 'bg-transparent', false: 'bg-black', }; +const smallInputClasses = { + true: 'input-small', + false: '' +} + const Input = ({ id, label, @@ -18,6 +23,7 @@ const Input = ({ labelClassName = '', className = '', transparent = false, + smallInput = false, type = 'text', value, onChange, @@ -39,6 +45,7 @@ const Input = ({ className, baseInputClasses, transparentClasses[transparent], + smallInputClasses[smallInput], { 'cursor-not-allowed': disabled } )} disabled={disabled} @@ -63,6 +70,7 @@ Input.propTypes = { labelClassName: PropTypes.string, className: PropTypes.string, transparent: PropTypes.bool, + smallInput: PropTypes.bool, type: PropTypes.string, value: PropTypes.any, onChange: PropTypes.func, diff --git a/platform/ui/src/components/Input/__stories__/input.stories.mdx b/platform/ui/src/components/Input/__stories__/input.stories.mdx index f4cdc174b..aab4caf63 100644 --- a/platform/ui/src/components/Input/__stories__/input.stories.mdx +++ b/platform/ui/src/components/Input/__stories__/input.stories.mdx @@ -53,6 +53,19 @@ Input is a component that renders the Inputs. +### Small Input + + + + {InputTemplate.bind({})} + + + ### Classnames You can change the appearance of the container and label. diff --git a/platform/ui/src/components/InputNumber/InputNumber.css b/platform/ui/src/components/InputNumber/InputNumber.css index 22f0c1ca1..8eae97b2e 100644 --- a/platform/ui/src/components/InputNumber/InputNumber.css +++ b/platform/ui/src/components/InputNumber/InputNumber.css @@ -2,7 +2,7 @@ input[type='text'] { -webkit-appearance: none; } -input[type='text']:focus { +.input-number:focus { border: none; outline: none; } @@ -15,3 +15,7 @@ input[type='text']:focus { .up-arrowsize svg path { fill: #726f7e; } + +.input-small { + height: 26px; +} diff --git a/platform/ui/src/components/InputNumber/InputNumber.tsx b/platform/ui/src/components/InputNumber/InputNumber.tsx index a96446293..c7ef97868 100644 --- a/platform/ui/src/components/InputNumber/InputNumber.tsx +++ b/platform/ui/src/components/InputNumber/InputNumber.tsx @@ -77,16 +77,15 @@ const InputNumber: React.FC<{ return (
diff --git a/platform/ui/src/components/InputText/InputText.tsx b/platform/ui/src/components/InputText/InputText.tsx index 2f5c1bb18..e5d95d81f 100644 --- a/platform/ui/src/components/InputText/InputText.tsx +++ b/platform/ui/src/components/InputText/InputText.tsx @@ -21,7 +21,7 @@ const InputText = ({ > {}, + onLabelClick: () => { }, sortDirection: 'none', }; diff --git a/platform/ui/tailwind.config.js b/platform/ui/tailwind.config.js index 90b0c2f99..1bce56ab0 100644 --- a/platform/ui/tailwind.config.js +++ b/platform/ui/tailwind.config.js @@ -35,6 +35,13 @@ module.exports = { active: '#348cfd', }, + inputfield: { + main: '#3a3f99', + disabled: '#2b166b', + focus: '#5acce6', + placeholder: '#39383f' + }, + secondary: { light: '#3a3f99', main: '#2b166b', diff --git a/platform/viewer/tailwind.config.js b/platform/viewer/tailwind.config.js index 535239ca5..272ff180c 100644 --- a/platform/viewer/tailwind.config.js +++ b/platform/viewer/tailwind.config.js @@ -46,6 +46,13 @@ module.exports = { active: '#348cfd', }, + inputfield: { + main: '#3a3f99', + disabled: '#2b166b', + focus: '#5acce6', + placeholder: '#39383f' + }, + secondary: { light: '#3a3f99', main: '#2b166b', From c9d3c08cb66e8d593ac0f9b084da872f028010a0 Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 28 Apr 2023 10:14:14 -0400 Subject: [PATCH 20/54] feat(cst): Add new command to get nearby annotation tools (#3327) * feat(cst): Add new command to get nearby annotation tools This commit adds a new command `getNearbyAnnotation` to the `commandsModule.ts` file that identifies nearby annotation tools excluding Crosshairs and ReferenceLines. It also removes an unused mapping to `Crosshairs` in `initMeasurementService.js` and changes the command run in `findNearbyToolData.ts` to `getNearbyAnnotation`. * perf(cornerstone): Improve performance by optimizing tools Removes unnecessary imports to improve app's performance. Changes how annotations are detected on the `commandsModule.js` file by fetching the `isAnnotation` property of the tool instance if available. Updates `CrosshairsTool` and `ReferenceLinesTool` to not be annotations anymore. Adjusts the `localhost` URL ports for the `dcm4chee-arc` service interface on `local_dcm4chee.js` to allow for more efficient server communication. * feat(cornerstone): Add CornerstoneServices type and ToolGroupService.getToolGroup to get tool group by ID or active viewport This commit introduces the new CornerstoneServices interface to the code and adds the ToolGroupService.getToolGroup method, which can retrieve a specific tool group by ID or from the active viewport. The older _getToolGroup method has also been removed from commandsModule. When no tool group ID is provided, this method now retrieves the tool group from the currently active viewport with the help of getActiveViewportEnabledElement. Additionally, the required reference to @ohif/core has been removed. --- extensions/cornerstone/src/commandsModule.ts | 80 +++++++++---------- .../cornerstone/src/initCornerstoneTools.js | 3 + .../cornerstone/src/initMeasurementService.js | 14 ---- .../ToolGroupService/ToolGroupService.ts | 49 ++++++++++-- .../src/utils/findNearbyToolData.ts | 2 +- .../MeasurementService/MeasurementService.ts | 3 +- .../viewer/public/config/local_dcm4chee.js | 7 +- 7 files changed, 90 insertions(+), 68 deletions(-) diff --git a/extensions/cornerstone/src/commandsModule.ts b/extensions/cornerstone/src/commandsModule.ts index 4d1948de8..c57d3b0a9 100644 --- a/extensions/cornerstone/src/commandsModule.ts +++ b/extensions/cornerstone/src/commandsModule.ts @@ -10,7 +10,6 @@ import { utilities as cstUtils, ReferenceLinesTool, } from '@cornerstonejs/tools'; -import { ServicesManager } from '@ohif/core'; import CornerstoneViewportDownloadForm from './utils/CornerstoneViewportDownloadForm'; import callInputDialog from './utils/callInputDialog'; @@ -18,6 +17,7 @@ import { setColormap } from './utils/colormap/transferFunctionHelpers'; import toggleStackImageSync from './utils/stackSync/toggleStackImageSync'; import { getFirstAnnotationSelected } from './utils/measurementServiceMappings/utils/selection'; import getActiveViewportEnabledElement from './utils/getActiveViewportEnabledElement'; +import { CornerstoneServices } from './types'; function commandsModule({ servicesManager, commandsManager }) { const { @@ -28,51 +28,14 @@ function commandsModule({ servicesManager, commandsManager }) { uiDialogService, cornerstoneViewportService, uiNotificationService, - customizationService, measurementService, - hangingProtocolService, - } = (servicesManager as ServicesManager).services; + } = servicesManager.services as CornerstoneServices; const { measurementServiceSource } = this; function _getActiveViewportEnabledElement() { return getActiveViewportEnabledElement(viewportGridService); } - - function _getToolGroup(toolGroupId) { - let toolGroupIdToUse = toolGroupId; - - if (!toolGroupIdToUse) { - // Use the active viewport's tool group if no tool group id is provided - const enabledElement = _getActiveViewportEnabledElement(); - - if (!enabledElement) { - return; - } - - const { renderingEngineId, viewportId } = enabledElement; - const toolGroup = ToolGroupManager.getToolGroupForViewport( - viewportId, - renderingEngineId - ); - - if (!toolGroup) { - console.warn( - 'No tool group found for viewportId:', - viewportId, - 'and renderingEngineId:', - renderingEngineId - ); - return; - } - - toolGroupIdToUse = toolGroup.id; - } - - const toolGroup = toolGroupService.getToolGroup(toolGroupIdToUse); - return toolGroup; - } - const actions = { /** * Generates the selector props for the context menu, specific to @@ -127,6 +90,36 @@ function commandsModule({ servicesManager, commandsManager }) { cstUtils.getAnnotationNearPoint(element, canvasCoordinates) ); }, + getNearbyAnnotation({ element, canvasCoordinates }) { + const nearbyToolData = actions.getNearbyToolData({ + nearbyToolData: null, + element, + canvasCoordinates, + }); + + const isAnnotation = toolName => { + const enabledElement = getEnabledElement(element); + + if (!enabledElement) { + return; + } + + const { renderingEngineId, viewportId } = enabledElement; + const toolGroup = ToolGroupManager.getToolGroupForViewport( + viewportId, + renderingEngineId + ); + + const toolInstance = toolGroup.getToolInstance(toolName); + + return toolInstance?.constructor?.isAnnotation ?? true; + }; + + return nearbyToolData?.metadata?.toolName && + isAnnotation(nearbyToolData.metadata.toolName) + ? nearbyToolData + : null; + }, // Measurement tool commands: @@ -298,7 +291,7 @@ function commandsModule({ servicesManager, commandsManager }) { setToolActive: ({ toolName, toolGroupId = null }) => { if (toolName === 'Crosshairs') { - const activeViewportToolGroup = _getToolGroup(null); + const activeViewportToolGroup = toolGroupService.getToolGroup(null); if (!activeViewportToolGroup._toolInstances.Crosshairs) { uiNotificationService.show({ @@ -317,7 +310,7 @@ function commandsModule({ servicesManager, commandsManager }) { viewports: [], }; - const toolGroup = _getToolGroup(toolGroupId); + const toolGroup = toolGroupService.getToolGroup(toolGroupId); const toolGroupViewportIds = toolGroup?.getViewportIds?.(); // if toolGroup has been destroyed, or its viewports have been removed @@ -635,6 +628,11 @@ function commandsModule({ servicesManager, commandsManager }) { storeContexts: [], options: {}, }, + getNearbyAnnotation: { + commandFn: actions.getNearbyAnnotation, + storeContexts: [], + options: {}, + }, deleteMeasurement: { commandFn: actions.deleteMeasurement, diff --git a/extensions/cornerstone/src/initCornerstoneTools.js b/extensions/cornerstone/src/initCornerstoneTools.js index 5df8f8983..9549b17f9 100644 --- a/extensions/cornerstone/src/initCornerstoneTools.js +++ b/extensions/cornerstone/src/initCornerstoneTools.js @@ -30,6 +30,9 @@ import { import CalibrationLineTool from './tools/CalibrationLineTool'; export default function initCornerstoneTools(configuration = {}) { + CrosshairsTool.isAnnotation = false; + ReferenceLinesTool.isAnnotation = false; + init(configuration); addTool(PanTool); addTool(WindowLevelTool); diff --git a/extensions/cornerstone/src/initMeasurementService.js b/extensions/cornerstone/src/initMeasurementService.js index c11a53111..3a883cc79 100644 --- a/extensions/cornerstone/src/initMeasurementService.js +++ b/extensions/cornerstone/src/initMeasurementService.js @@ -49,20 +49,6 @@ const initMeasurementService = ( Length.toMeasurement ); - measurementService.addMapping( - csTools3DVer1MeasurementSource, - 'Crosshairs', - Length.matchingCriteria, - () => { - console.warn('Crosshairs mapping not implemented.'); - return {}; - }, - () => { - console.warn('Crosshairs mapping not implemented.'); - return {}; - } - ); - measurementService.addMapping( csTools3DVer1MeasurementSource, 'Bidirectional', diff --git a/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts b/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts index 4f5512ecf..8772e02bf 100644 --- a/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts +++ b/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts @@ -1,6 +1,7 @@ import { ToolGroupManager, Enums, Types } from '@cornerstonejs/tools'; import { Types as OhifTypes, pubSubServiceInterface } from '@ohif/core'; +import getActiveViewportEnabledElement from '../../utils/getActiveViewportEnabledElement'; const EVENTS = { VIEWPORT_ADDED: 'event::cornerstone::toolgroupservice:viewportadded', @@ -39,20 +40,56 @@ export default class ToolGroupService { EVENTS: { [key: string]: string }; constructor(serviceManager) { - const { cornerstoneViewportService } = serviceManager.services; + const { + cornerstoneViewportService, + viewportGridService, + } = serviceManager.services; this.cornerstoneViewportService = cornerstoneViewportService; + this.viewportGridService = viewportGridService; this.listeners = {}; this.EVENTS = EVENTS; Object.assign(this, pubSubServiceInterface); } /** - * Returns the cornerstone ToolGroup for a given toolGroup UID - * @param {string} toolGroupId - The toolGroup uid - * @returns {IToolGroup} - The toolGroup + * Retrieves a tool group from the ToolGroupManager by tool group ID. + * If no tool group ID is provided, it retrieves the tool group of the active viewport. + * @param toolGroupId - Optional ID of the tool group to retrieve. + * @returns The tool group or undefined if it is not found. */ - public getToolGroup(toolGroupId: string): Types.IToolGroup | void { - const toolGroup = ToolGroupManager.getToolGroup(toolGroupId); + public getToolGroup(toolGroupId?: string): Types.IToolGroup | void { + let toolGroupIdToUse = toolGroupId; + + if (!toolGroupIdToUse) { + // Use the active viewport's tool group if no tool group id is provided + const enabledElement = getActiveViewportEnabledElement( + this.viewportGridService + ); + + if (!enabledElement) { + return; + } + + const { renderingEngineId, viewportId } = enabledElement; + const toolGroup = ToolGroupManager.getToolGroupForViewport( + viewportId, + renderingEngineId + ); + + if (!toolGroup) { + console.warn( + 'No tool group found for viewportId:', + viewportId, + 'and renderingEngineId:', + renderingEngineId + ); + return; + } + + toolGroupIdToUse = toolGroup.id; + } + + const toolGroup = ToolGroupManager.getToolGroup(toolGroupIdToUse); return toolGroup; } diff --git a/extensions/cornerstone/src/utils/findNearbyToolData.ts b/extensions/cornerstone/src/utils/findNearbyToolData.ts index ab57a67d2..95e934766 100644 --- a/extensions/cornerstone/src/utils/findNearbyToolData.ts +++ b/extensions/cornerstone/src/utils/findNearbyToolData.ts @@ -11,7 +11,7 @@ export const findNearbyToolData = (commandsManager, evt) => { } const { element, currentPoints } = evt.detail; return commandsManager.runCommand( - 'getNearbyToolData', + 'getNearbyAnnotation', { element, canvasCoordinates: currentPoints?.canvas, diff --git a/platform/core/src/services/MeasurementService/MeasurementService.ts b/platform/core/src/services/MeasurementService/MeasurementService.ts index 3a89d2094..b1d3e5af7 100644 --- a/platform/core/src/services/MeasurementService/MeasurementService.ts +++ b/platform/core/src/services/MeasurementService/MeasurementService.ts @@ -508,7 +508,6 @@ class MeasurementService extends PubSubService { if (!this._isValidSource(source)) { throw new Error('Invalid source.'); } - if (!annotationType) { throw new Error('No source annotationType provided.'); } @@ -572,7 +571,7 @@ class MeasurementService extends PubSubService { // For now, it is just added in OHIF here and in setMeasurementSelected. this.measurements[internalUID] = newMeasurement; if (isUpdate) { - this._broadcastEvent(this.EVENTS.MEASUREMENT_UPDATED, { + this._broadcastEvent(this.EVENTS.MEASUREMENT_UPDATED, { source, measurement: newMeasurement, notYetUpdatedAtSource: false, diff --git a/platform/viewer/public/config/local_dcm4chee.js b/platform/viewer/public/config/local_dcm4chee.js index 28ae28fd9..fca1f2a71 100644 --- a/platform/viewer/public/config/local_dcm4chee.js +++ b/platform/viewer/public/config/local_dcm4chee.js @@ -16,14 +16,13 @@ window.config = { sourceName: 'dicomweb', configuration: { name: 'DCM4CHEE', - wadoUriRoot: 'http://localhost/dcm4chee-arc/aets/DCM4CHEE/wado', - qidoRoot: 'http://localhost/dcm4chee-arc/aets/DCM4CHEE/rs', - wadoRoot: 'http://localhost/dcm4chee-arc/aets/DCM4CHEE/rs', + wadoUriRoot: 'http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/wado', + qidoRoot: 'http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs', + wadoRoot: 'http://localhost:8080/dcm4chee-arc/aets/DCM4CHEE/rs', qidoSupportsIncludeField: true, imageRendering: 'wadors', enableStudyLazyLoad: true, thumbnailRendering: 'wadors', - useBulkDataURI: false, requestOptions: { auth: 'admin:admin', }, From f377153b60157883f0c15473126a2d666b910713 Mon Sep 17 00:00:00 2001 From: Alireza Date: Fri, 28 Apr 2023 11:06:03 -0400 Subject: [PATCH 21/54] fix(viewportDialog): viewportDialoge not appearing in non-tracked viewports (#3071) * fix: viewportdialoge not appearing in non-tracked viewports * feat(viewports): Introduce useViewportDialog and remove deprecated API This commit introduces the `useViewportDialog` hook and replaces the deprecated `viewportDialogApi` with the new `viewportDialogState`. Additionally, the notifications in `OHIFCornerstoneRTViewport` and `OHIFCornerstoneViewport` have been removed. Finally, the `CinePlayer` component now accepts optional parameters. * fix tests --- .../viewports/OHIFCornerstoneRTViewport.tsx | 15 --- .../viewports/OHIFCornerstoneSEGViewport.tsx | 15 --- .../viewports/OHIFCornerstoneSRViewport.tsx | 11 -- .../src/Viewport/OHIFCornerstoneViewport.tsx | 111 +++++++++++------- .../viewports/TrackedCornerstoneViewport.tsx | 12 -- .../src/components/CinePlayer/CinePlayer.tsx | 16 +-- .../OHIFCornerstoneToolbar.spec.js | 8 +- .../OHIFMeasurementPanel.spec.js | 8 +- 8 files changed, 78 insertions(+), 118 deletions(-) diff --git a/extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx b/extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx index 29adb47d5..b7708968c 100644 --- a/extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx +++ b/extensions/cornerstone-dicom-rt/src/viewports/OHIFCornerstoneRTViewport.tsx @@ -2,10 +2,8 @@ import React, { useCallback, useEffect, useRef, useState } from 'react'; import PropTypes from 'prop-types'; import OHIF, { utils } from '@ohif/core'; import { - Notification, ViewportActionBar, useViewportGrid, - useViewportDialog, LoadingIndicatorTotalPercent, } from '@ohif/ui'; @@ -47,7 +45,6 @@ function OHIFCornerstoneRTViewport(props) { const rtDisplaySet = displaySets[0]; const [viewportGrid, viewportGridService] = useViewportGrid(); - const [viewportDialogState, viewportDialogApi] = useViewportDialog(); // States const [isToolGroupCreated, setToolGroupCreated] = useState(false); @@ -363,18 +360,6 @@ function OHIFCornerstoneRTViewport(props) { /> )} {getCornerstoneViewport()} -
- {viewportDialogState.viewportIndex === viewportIndex && ( - - )} -
{childrenWithProps}
diff --git a/extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx b/extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx index e901ac0be..08ed004f0 100644 --- a/extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx +++ b/extensions/cornerstone-dicom-seg/src/viewports/OHIFCornerstoneSEGViewport.tsx @@ -4,8 +4,6 @@ import { useTranslation } from 'react-i18next'; import OHIF, { utils } from '@ohif/core'; import { LoadingIndicatorTotalPercent, - Notification, - useViewportDialog, useViewportGrid, ViewportActionBar, } from '@ohif/ui'; @@ -48,7 +46,6 @@ function OHIFCornerstoneSEGViewport(props) { const segDisplaySet = displaySets[0]; const [viewportGrid, viewportGridService] = useViewportGrid(); - const [viewportDialogState, viewportDialogApi] = useViewportDialog(); // States const [isToolGroupCreated, setToolGroupCreated] = useState(false); @@ -366,18 +363,6 @@ function OHIFCornerstoneSEGViewport(props) { /> )} {getCornerstoneViewport()} -
- {viewportDialogState.viewportIndex === viewportIndex && ( - - )} -
{childrenWithProps}
diff --git a/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx b/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx index 75b34893f..4ef8f2bdf 100644 --- a/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx +++ b/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx @@ -401,17 +401,6 @@ function OHIFCornerstoneSRViewport(props) {
{getCornerstoneViewport()} -
- {viewportDialogState.viewportIndex === viewportIndex && ( - - )} -
{childrenWithProps}
diff --git a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx index d74a3b99b..1071814bc 100644 --- a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx +++ b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx @@ -8,9 +8,14 @@ import { getEnabledElement, StackViewport, utilities as csUtils, - CONSTANTS, } from '@cornerstonejs/core'; -import { CinePlayer, useCine, useViewportGrid } from '@ohif/ui'; +import { + CinePlayer, + useCine, + useViewportGrid, + Notification, + useViewportDialog, +} from '@ohif/ui'; import { IStackViewport, IVolumeViewport, @@ -132,6 +137,8 @@ const OHIFCornerstoneViewport = React.memo(props => { stateSyncService, } = servicesManager.services as CornerstoneServices; + const [viewportDialogState] = useViewportDialog(); + const cineHandler = () => { if (!cines || !cines[viewportIndex] || !enabledVPElement) { return; @@ -455,50 +462,64 @@ const OHIFCornerstoneViewport = React.memo(props => { }, [displaySets, elementRef, viewportIndex]); return ( -
- -
e.preventDefault()} - onMouseDown={e => e.preventDefault()} - ref={elementRef} - >
- - {isCineEnabled && ( - - cineService.setCine({ - id: activeViewportIndex, - isPlaying, - }) - } - onFrameRateChange={frameRate => - cineService.setCine({ - id: activeViewportIndex, - frameRate, - }) - } + +
+ - )} -
+
e.preventDefault()} + onMouseDown={e => e.preventDefault()} + ref={elementRef} + >
+ + {isCineEnabled && ( + + cineService.setCine({ + id: activeViewportIndex, + isPlaying, + }) + } + onFrameRateChange={frameRate => + cineService.setCine({ + id: activeViewportIndex, + frameRate, + }) + } + /> + )} +
+
+ {viewportDialogState.viewportIndex === viewportIndex && ( + + )} +
+ ); }, areEqual); diff --git a/extensions/measurement-tracking/src/viewports/TrackedCornerstoneViewport.tsx b/extensions/measurement-tracking/src/viewports/TrackedCornerstoneViewport.tsx index 5e5393f53..47da82c8b 100644 --- a/extensions/measurement-tracking/src/viewports/TrackedCornerstoneViewport.tsx +++ b/extensions/measurement-tracking/src/viewports/TrackedCornerstoneViewport.tsx @@ -159,18 +159,6 @@ function TrackedCornerstoneViewport(props) { {/* TODO: Viewport interface to accept stack or layers of content like this? */}
{getCornerstoneViewport()} -
- {viewportDialogState.viewportIndex === viewportIndex && ( - - )} -
); diff --git a/platform/ui/src/components/CinePlayer/CinePlayer.tsx b/platform/ui/src/components/CinePlayer/CinePlayer.tsx index 6ede1bf11..7c52b47fd 100644 --- a/platform/ui/src/components/CinePlayer/CinePlayer.tsx +++ b/platform/ui/src/components/CinePlayer/CinePlayer.tsx @@ -9,10 +9,10 @@ import classNames from 'classnames'; export type CinePlayerProps = { className: string; isPlaying: boolean; - minFrameRate: number; - maxFrameRate: number; - stepFrameRate: number; - frameRate: number; + minFrameRate?: number; + maxFrameRate?: number; + stepFrameRate?: number; + frameRate?: number; onFrameRateChange: (value: number) => void; onPlayPauseChange: (value: boolean) => void; onClose: () => void; @@ -116,12 +116,12 @@ CinePlayer.defaultProps = { CinePlayer.propTypes = { /** Minimum value for range slider */ - minFrameRate: PropTypes.number.isRequired, + minFrameRate: PropTypes.number, /** Maximum value for range slider */ - maxFrameRate: PropTypes.number.isRequired, + maxFrameRate: PropTypes.number, /** Increment range slider can "step" in either direction */ - stepFrameRate: PropTypes.number.isRequired, - frameRate: PropTypes.number.isRequired, + stepFrameRate: PropTypes.number, + frameRate: PropTypes.number, /** 'true' if playing, 'false' if paused */ isPlaying: PropTypes.bool.isRequired, onPlayPauseChange: PropTypes.func, diff --git a/platform/viewer/cypress/integration/measurement-tracking/OHIFCornerstoneToolbar.spec.js b/platform/viewer/cypress/integration/measurement-tracking/OHIFCornerstoneToolbar.spec.js index aba69f17f..c20aa75c6 100644 --- a/platform/viewer/cypress/integration/measurement-tracking/OHIFCornerstoneToolbar.spec.js +++ b/platform/viewer/cypress/integration/measurement-tracking/OHIFCornerstoneToolbar.spec.js @@ -111,12 +111,8 @@ describe('OHIF Cornerstone Toolbar', () => { it('checks if Length annotation can be added to viewport and shows up in the measurements panel', () => { //Click on button and verify if icon is active on toolbar cy.addLengthMeasurement(); - cy.get('[data-cy="measurement-tracking-prompt-begin-tracking"]').should( - 'exist' - ); - cy.get('[data-cy="measurement-tracking-prompt-begin-tracking"]').should( - 'be.visible' - ); + cy.get('[data-cy="viewport-notification"]').should('exist'); + cy.get('[data-cy="viewport-notification"]').should('be.visible'); cy.get('[data-cy="prompt-begin-tracking-yes"]').click(); //Verify the measurement exists in the table diff --git a/platform/viewer/cypress/integration/measurement-tracking/OHIFMeasurementPanel.spec.js b/platform/viewer/cypress/integration/measurement-tracking/OHIFMeasurementPanel.spec.js index d380d9544..c96d77701 100644 --- a/platform/viewer/cypress/integration/measurement-tracking/OHIFMeasurementPanel.spec.js +++ b/platform/viewer/cypress/integration/measurement-tracking/OHIFMeasurementPanel.spec.js @@ -25,12 +25,8 @@ describe('OHIF Measurement Panel', function() { it('checks if measurement item can be Relabeled under Measurements panel', function() { // Add length measurement cy.addLengthMeasurement(); - cy.get('[data-cy="measurement-tracking-prompt-begin-tracking"]').should( - 'exist' - ); - cy.get('[data-cy="measurement-tracking-prompt-begin-tracking"]').should( - 'be.visible' - ); + cy.get('[data-cy="viewport-notification"]').should('exist'); + cy.get('[data-cy="viewport-notification"]').should('be.visible'); cy.get('[data-cy="prompt-begin-tracking-yes"]').click(); cy.get('[data-cy="measurement-item"]').click(); From 66f6e3eade5708c8e03d788ebfbe9429a5ffdd81 Mon Sep 17 00:00:00 2001 From: Joe Boccanfuso <109477394+jbocce@users.noreply.github.com> Date: Fri, 28 Apr 2023 16:13:47 -0400 Subject: [PATCH 22/54] feat(DICOM Upload): Added new DICOM upload dialogue launched from the worklist page (#3326) * feat(DICOM Upload) OHIF #3297 - DicomWebDataSource.store.dicom now accepts an ArrayBuffer of data sets to store - DicomWebDataSource.store.dicom now also accepts optional callbacks to track upload and an AbortSignal object to cancel upload - Added DicomFileUploader class that performs and tracks the upload of a DICOM file - Added various UI pieces for the upload: DicomUpload, DicomUploadProgress, DicomUploadProgressItem - ProgressLoadingBar was extracted from LoadingIndicatorProgress so it can be reused - Modal dialogues can now optionally prevent an outside click from closing the Modal * Passing an XMLHttpRequest to the dataSource.store.dicom method instead of callbacks and AbortSignal. Cleanup of various UI pieces to minimize code and increase readability. * Made the DicomUpload component a customization module exported by the cornerstone extension. * Exposed a copy of the data source configuration via the IWebApiDataSource interface. Added dicomUploadEnabled to a data source's configuration. * Code clean up. * Upgraded the dicomweb-client version to one that provides the ability to pass a custom HTTP request. DICOM upload uses that custom HTTP request to track progress and cancel requests. * Distinguished between failed and cancelled uploads. * Allow no selection in the upload dialogue. Fixed the styling of various progress information so that everything aligns. * Switched from cornerstone wado image loader to cornerstone dicom image loader for DICOM upload. * Added special cancelled icon to differentiate from failed. * Added a bit of spacing between the upload progress bar and percentage. * Fixed minor issue with upload rejection. * Performance improvement for cancel all uploads: - use React memo for each upload item progress (row) - do not await each request of a cancel all * Fixed various padding/spacing for the DICOM upload drop zone component. Changed the border dashing for the DICOM upload drop zone to be a background image gradient. Added hover and active effects to the 'Cancel All Uploads' text. --- .../components/DicomUpload/DicomUpload.css | 6 + .../components/DicomUpload/DicomUpload.tsx | 116 +++++ .../DicomUpload/DicomUploadProgress.tsx | 436 ++++++++++++++++++ .../DicomUpload/DicomUploadProgressItem.tsx | 117 +++++ .../cornerstone/src/getCustomizationModule.ts | 8 + .../src/utils/DicomFileUploader.ts | 220 +++++++++ extensions/default/package.json | 2 +- .../default/src/DicomWebDataSource/index.js | 52 ++- platform/core/package.json | 2 +- .../core/src/DataSources/IWebApiDataSource.js | 7 + .../ui/src/assets/icons/icon-alert-small.svg | 8 + .../ui/src/assets/icons/icon-status-alert.svg | 8 + .../ui/src/assets/icons/icon-transferring.svg | 6 + platform/ui/src/assets/icons/icon-upload.svg | 6 + .../src/assets/icons/icons-alert-outline.svg | 8 + platform/ui/src/components/Button/Button.tsx | 4 + platform/ui/src/components/Icon/getIcon.js | 10 + .../LoadingIndicatorProgress.tsx | 17 +- platform/ui/src/components/Modal/Modal.tsx | 4 + .../ProgressLoadingBar.css} | 10 +- .../ProgressLoadingBar/ProgressLoadingBar.tsx | 34 ++ .../components/ProgressLoadingBar/index.js | 2 + .../StudyListFilter/StudyListFilter.tsx | 11 + platform/ui/src/components/index.js | 2 + .../ui/src/contextProviders/ModalProvider.tsx | 10 +- platform/ui/src/index.js | 1 + .../viewer/public/config/local_dcm4chee.js | 5 + .../viewer/public/config/local_orthanc.js | 5 + .../viewer/src/routes/DataSourceWrapper.tsx | 7 +- .../viewer/src/routes/WorkList/WorkList.tsx | 34 +- platform/viewer/src/routes/index.tsx | 13 +- yarn.lock | 305 +----------- 32 files changed, 1126 insertions(+), 350 deletions(-) create mode 100644 extensions/cornerstone/src/components/DicomUpload/DicomUpload.css create mode 100644 extensions/cornerstone/src/components/DicomUpload/DicomUpload.tsx create mode 100644 extensions/cornerstone/src/components/DicomUpload/DicomUploadProgress.tsx create mode 100644 extensions/cornerstone/src/components/DicomUpload/DicomUploadProgressItem.tsx create mode 100644 extensions/cornerstone/src/utils/DicomFileUploader.ts create mode 100644 platform/ui/src/assets/icons/icon-alert-small.svg create mode 100644 platform/ui/src/assets/icons/icon-status-alert.svg create mode 100644 platform/ui/src/assets/icons/icon-transferring.svg create mode 100644 platform/ui/src/assets/icons/icon-upload.svg create mode 100644 platform/ui/src/assets/icons/icons-alert-outline.svg rename platform/ui/src/components/{LoadingIndicatorProgress/LoadingIndicatorProgress.css => ProgressLoadingBar/ProgressLoadingBar.css} (71%) create mode 100644 platform/ui/src/components/ProgressLoadingBar/ProgressLoadingBar.tsx create mode 100644 platform/ui/src/components/ProgressLoadingBar/index.js diff --git a/extensions/cornerstone/src/components/DicomUpload/DicomUpload.css b/extensions/cornerstone/src/components/DicomUpload/DicomUpload.css new file mode 100644 index 000000000..55ddf7922 --- /dev/null +++ b/extensions/cornerstone/src/components/DicomUpload/DicomUpload.css @@ -0,0 +1,6 @@ +.dicom-upload-drop-area-border-dash { + background-image: repeating-linear-gradient(to right, #7BB2CE 0%, #7BB2CE 50%, transparent 50%, transparent 100%), repeating-linear-gradient(to right, #7BB2CE 0%, #7BB2CE 50%, transparent 50%, transparent 100%), repeating-linear-gradient(to bottom, #7BB2CE 0%, #7BB2CE 50%, transparent 50%, transparent 100%), repeating-linear-gradient(to bottom, #7BB2CE 0%, #7BB2CE 50%, transparent 50%, transparent 100%); + background-position: left top, left bottom, left top, right top; + background-repeat: repeat-x, repeat-x, repeat-y, repeat-y; + background-size: 20px 3px, 20px 3px, 3px 20px, 3px 20px; +} diff --git a/extensions/cornerstone/src/components/DicomUpload/DicomUpload.tsx b/extensions/cornerstone/src/components/DicomUpload/DicomUpload.tsx new file mode 100644 index 000000000..fa29e65d1 --- /dev/null +++ b/extensions/cornerstone/src/components/DicomUpload/DicomUpload.tsx @@ -0,0 +1,116 @@ +import React, { useCallback, useState } from 'react'; +import { ReactElement } from 'react'; +import Dropzone from 'react-dropzone'; +import PropTypes from 'prop-types'; +import classNames from 'classnames'; +import DicomFileUploader from '../../utils/DicomFileUploader'; +import DicomUploadProgress from './DicomUploadProgress'; +import { Button } from '@ohif/ui'; +import './DicomUpload.css'; + +type DicomUploadProps = { + dataSource; + onComplete: () => void; + onStarted: () => void; +}; + +function DicomUpload({ + dataSource, + onComplete, + onStarted, +}: DicomUploadProps): ReactElement { + const baseClassNames = 'min-h-[520px] flex flex-col bg-black select-none'; + const [dicomFileUploaderArr, setDicomFileUploaderArr] = useState([]); + + const onDrop = useCallback(async acceptedFiles => { + onStarted(); + setDicomFileUploaderArr( + acceptedFiles.map(file => new DicomFileUploader(file, dataSource)) + ); + }, []); + + const getDropZoneComponent = (): ReactElement => { + return ( + { + onDrop(acceptedFiles); + }} + noClick + > + {({ getRootProps }) => ( +
+
+ + {({ getRootProps, getInputProps }) => ( +
+ +
+ )} + + + {({ getRootProps, getInputProps }) => ( +
+ +
+ )} + +
+
or drag images or folders here
+
+ (DICOM files supported) +
+
+ )} + + ); + }; + + return ( + <> + {dicomFileUploaderArr.length ? ( +
+ +
+ ) : ( +
+ {getDropZoneComponent()} +
+ )} + + ); +} + +DicomUpload.propTypes = { + dataSource: PropTypes.object.isRequired, + onComplete: PropTypes.func.isRequired, + onStarted: PropTypes.func.isRequired, +}; + +export default DicomUpload; diff --git a/extensions/cornerstone/src/components/DicomUpload/DicomUploadProgress.tsx b/extensions/cornerstone/src/components/DicomUpload/DicomUploadProgress.tsx new file mode 100644 index 000000000..f1b2de731 --- /dev/null +++ b/extensions/cornerstone/src/components/DicomUpload/DicomUploadProgress.tsx @@ -0,0 +1,436 @@ +import React, { + useCallback, + useEffect, + useRef, + useState, + ReactElement, +} from 'react'; +import PropTypes from 'prop-types'; +import { Button, Icon, ProgressLoadingBar } from '@ohif/ui'; +import DicomFileUploader, { + EVENTS, + UploadStatus, + DicomFileUploaderProgressEvent, + UploadRejection, +} from '../../utils/DicomFileUploader'; +import DicomUploadProgressItem from './DicomUploadProgressItem'; +import classNames from 'classnames'; + +type DicomUploadProgressProps = { + dicomFileUploaderArr: DicomFileUploader[]; + onComplete: () => void; +}; + +const ONE_SECOND = 1000; +const ONE_MINUTE = ONE_SECOND * 60; +const ONE_HOUR = ONE_MINUTE * 60; + +// The base/initial interval time length used to calculate the +// rate of the upload and in turn estimate the +// the amount of time remaining for the upload. This is the length +// of the very first interval to get a reasonable estimate on screen in +// a reasonable amount of time. The length of each interval after the first +// is based on the upload rate calculated. Faster rates use this base interval +// length. Slower rates below UPLOAD_RATE_THRESHOLD get longer interval times +// to obtain more accurate upload rates. +const BASE_INTERVAL_TIME = 15000; + +// The upload rate threshold to determine the length of the interval to +// calculate the upload rate. +const UPLOAD_RATE_THRESHOLD = 75; + +const NO_WRAP_ELLIPSIS_CLASS_NAMES = + 'text-ellipsis whitespace-nowrap overflow-hidden'; + +function DicomUploadProgress({ + dicomFileUploaderArr, + onComplete, +}: DicomUploadProgressProps): ReactElement { + const [totalUploadSize] = useState( + dicomFileUploaderArr.reduce( + (acc, fileUploader) => acc + fileUploader.getFileSize(), + 0 + ) + ); + + const currentUploadSizeRef = useRef(0); + + const uploadRateRef = useRef(0); + + const [timeRemaining, setTimeRemaining] = useState(null); + + const [percentComplete, setPercentComplete] = useState(0); + + const [numFilesCompleted, setNumFilesCompleted] = useState(0); + + const [numFails, setNumFails] = useState(0); + + const [showFailedOnly, setShowFailedOnly] = useState(false); + + const progressBarContainerRef = useRef(); + + /** + * The effect for measuring and setting the current upload rate. This is + * done by measuring the amount of data uploaded in a set interval time. + */ + useEffect(() => { + let timeoutId: NodeJS.Timeout; + + // The amount of data already uploaded at the start of the interval. + let intervalStartUploadSize = 0; + + // The starting time of the interval. + let intervalStartTime = Date.now(); + + const setUploadRateRef = () => { + const uploadSizeFromStartOfInterval = + currentUploadSizeRef.current - intervalStartUploadSize; + + const now = Date.now(); + const timeSinceStartOfInterval = now - intervalStartTime; + + // Calculate and set the upload rate (ref) + uploadRateRef.current = + uploadSizeFromStartOfInterval / timeSinceStartOfInterval; + + // Reset the interval starting values. + intervalStartUploadSize = currentUploadSizeRef.current; + intervalStartTime = now; + + // Only start a new interval if there is more to upload. + if (totalUploadSize - currentUploadSizeRef.current > 0) { + if (uploadRateRef.current >= UPLOAD_RATE_THRESHOLD) { + timeoutId = setTimeout(setUploadRateRef, BASE_INTERVAL_TIME); + } else { + // The current upload rate is relatively slow, so use a larger + // time interval to get a better upload rate estimate. + timeoutId = setTimeout(setUploadRateRef, BASE_INTERVAL_TIME * 2); + } + } + }; + + // The very first interval is just the base time interval length. + timeoutId = setTimeout(setUploadRateRef, BASE_INTERVAL_TIME); + + return () => { + clearTimeout(timeoutId); + }; + }, []); + + /** + * The effect for: updating the overall percentage complete; setting the + * estimated time remaining; updating the number of files uploaded; and + * detecting if any error has occurred. + */ + useEffect(() => { + let currentTimeRemaining = null; + + // For each uploader, listen for the progress percentage complete and + // add promise catch/finally callbacks to detect errors and count number + // of uploads complete. + const subscriptions = dicomFileUploaderArr.map(fileUploader => { + let currentFileUploadSize = 0; + + const updateProgress = (percentComplete: number) => { + const previousFileUploadSize = currentFileUploadSize; + + currentFileUploadSize = Math.round( + (percentComplete / 100) * fileUploader.getFileSize() + ); + + currentUploadSizeRef.current = Math.min( + totalUploadSize, + currentUploadSizeRef.current - + previousFileUploadSize + + currentFileUploadSize + ); + + setPercentComplete( + (currentUploadSizeRef.current / totalUploadSize) * 100 + ); + + if (uploadRateRef.current !== 0) { + const uploadSizeRemaining = + totalUploadSize - currentUploadSizeRef.current; + + const timeRemaining = Math.round( + uploadSizeRemaining / uploadRateRef.current + ); + + if (currentTimeRemaining === null) { + currentTimeRemaining = timeRemaining; + setTimeRemaining(currentTimeRemaining); + return; + } + + // Do not show an increase in the time remaining by two seconds or minutes + // so as to prevent jumping the time remaining up and down constantly + // due to rounding, inaccuracies in the estimate and slight variations + // in upload rates over time. + if (timeRemaining < ONE_MINUTE) { + const currentSecondsRemaining = Math.ceil( + currentTimeRemaining / ONE_SECOND + ); + const secondsRemaining = Math.ceil(timeRemaining / ONE_SECOND); + const delta = secondsRemaining - currentSecondsRemaining; + if (delta < 0 || delta > 2) { + currentTimeRemaining = timeRemaining; + setTimeRemaining(currentTimeRemaining); + } + return; + } + + if (timeRemaining < ONE_HOUR) { + const currentMinutesRemaining = Math.ceil( + currentTimeRemaining / ONE_MINUTE + ); + const minutesRemaining = Math.ceil(timeRemaining / ONE_MINUTE); + const delta = minutesRemaining - currentMinutesRemaining; + if (delta < 0 || delta > 2) { + currentTimeRemaining = timeRemaining; + setTimeRemaining(currentTimeRemaining); + } + return; + } + + // Hours remaining... + currentTimeRemaining = timeRemaining; + setTimeRemaining(currentTimeRemaining); + } + }; + + const progressCallback = ( + progressEvent: DicomFileUploaderProgressEvent + ) => { + updateProgress(progressEvent.percentComplete); + }; + + // Use the uploader promise to flag any error and count the number of + // uploads completed. + fileUploader + .load() + .catch((rejection: UploadRejection) => { + if (rejection.status === UploadStatus.Failed) { + setNumFails(numFails => numFails + 1); + } + }) + .finally(() => { + // If any error occurred, the percent complete progress stops firing + // but this call to updateProgress nicely puts all finished uploads at 100%. + updateProgress(100); + setNumFilesCompleted(numCompleted => numCompleted + 1); + }); + + return fileUploader.subscribe(EVENTS.PROGRESS, progressCallback); + }); + return () => { + subscriptions.forEach(subscription => subscription.unsubscribe()); + }; + }, []); + + const cancelAllUploads = useCallback(async () => { + for (const dicomFileUploader of dicomFileUploaderArr) { + // Important: we need a non-blocking way to cancel every upload, + // otherwise the UI will freeze and the user will not be able + // to interact with the app and progress will not be updated. + const promise = new Promise((resolve, reject) => { + setTimeout(() => { + dicomFileUploader.cancel(); + resolve(); + }, 0); + }); + } + }, []); + + const getFormattedTimeRemaining = useCallback((): string => { + if (timeRemaining == null) { + return ''; + } + + if (timeRemaining < ONE_MINUTE) { + const secondsRemaining = Math.ceil(timeRemaining / ONE_SECOND); + return `${secondsRemaining} ${ + secondsRemaining === 1 ? 'second' : 'seconds' + }`; + } + + if (timeRemaining < ONE_HOUR) { + const minutesRemaining = Math.ceil(timeRemaining / ONE_MINUTE); + return `${minutesRemaining} ${ + minutesRemaining === 1 ? 'minute' : 'minutes' + }`; + } + + const hoursRemaining = Math.ceil(timeRemaining / ONE_HOUR); + return `${hoursRemaining} ${hoursRemaining === 1 ? 'hour' : 'hours'}`; + }, [timeRemaining]); + + const getPercentCompleteRounded = useCallback( + () => Math.min(100, Math.round(percentComplete)), + [percentComplete] + ); + + /** + * Determines if the progress bar should show the infinite animation or not. + * Show the infinite animation for progress less than 1% AND if less than + * one pixel of the progress bar would be displayed. + */ + const showInfiniteProgressBar = useCallback((): boolean => { + return ( + getPercentCompleteRounded() < 1 && + (progressBarContainerRef?.current?.offsetWidth ?? 0) * + (percentComplete / 100) < + 1 + ); + }, [getPercentCompleteRounded, percentComplete]); + + /** + * Gets the css style for the 'n of m' (files completed) text. The only css attribute + * of the style is width such that the 'n of m' is always a fixed width and thus + * as each file completes uploading the text on screen does not constantly shift + * left and right. + */ + const getNofMFilesStyle = useCallback(() => { + // the number of digits accounts for the digits being on each side of the ' of ' + const numDigits = 2 * dicomFileUploaderArr.length.toString().length; + // the number of digits + 2 spaces and 2 characters for ' of ' + const numChars = numDigits + 4; + return { width: `${numChars}ch` }; + }, []); + + const getNumCompletedAndTimeRemainingComponent = (): ReactElement => { + return ( +
+ {numFilesCompleted === dicomFileUploaderArr.length ? ( + <> + {`${ + dicomFileUploaderArr.length + } ${ + dicomFileUploaderArr.length > 1 ? 'files' : 'file' + } completed.`} + + + ) : ( + <> + + {`${numFilesCompleted} of ${dicomFileUploaderArr.length}`}  + + + {' files completed.'}  + + + {timeRemaining + ? `Less than ${getFormattedTimeRemaining()} remaining. ` + : ''} + + + Cancel All Uploads + + + )} +
+ ); + }; + + const getShowFailedOnlyIconComponent = (): ReactElement => { + return ( +
+ {numFails > 0 && ( +
+ setShowFailedOnly(currentShowFailedOnly => !currentShowFailedOnly) + } + > + +
+ )} +
+ ); + }; + + const getPercentCompleteComponent = (): ReactElement => { + return ( +
+
+ {numFilesCompleted === dicomFileUploaderArr.length ? ( + <> +
+ {numFails > 0 + ? `Completed with ${numFails} ${ + numFails > 1 ? 'errors' : 'error' + }!` + : 'Completed!'} +
+ {getShowFailedOnlyIconComponent()} + + ) : ( + <> +
+ +
+
+
{`${getPercentCompleteRounded()}%`}
+ {getShowFailedOnlyIconComponent()} +
+ + )} +
+
+ ); + }; + + return ( +
+ {getNumCompletedAndTimeRemainingComponent()} +
+ {getPercentCompleteComponent()} +
+ {dicomFileUploaderArr + .filter( + dicomFileUploader => + !showFailedOnly || + dicomFileUploader.getStatus() === UploadStatus.Failed + ) + .map(dicomFileUploader => ( + + ))} +
+
+
+ ); +} + +DicomUploadProgress.propTypes = { + dicomFileUploaderArr: PropTypes.arrayOf( + PropTypes.instanceOf(DicomFileUploader) + ).isRequired, + onComplete: PropTypes.func.isRequired, +}; + +export default DicomUploadProgress; diff --git a/extensions/cornerstone/src/components/DicomUpload/DicomUploadProgressItem.tsx b/extensions/cornerstone/src/components/DicomUpload/DicomUploadProgressItem.tsx new file mode 100644 index 000000000..bcbdcec58 --- /dev/null +++ b/extensions/cornerstone/src/components/DicomUpload/DicomUploadProgressItem.tsx @@ -0,0 +1,117 @@ +import React, { + ReactElement, + memo, + useCallback, + useEffect, + useState, +} from 'react'; +import PropTypes from 'prop-types'; +import DicomFileUploader, { + DicomFileUploaderProgressEvent, + EVENTS, + UploadRejection, + UploadStatus, +} from '../../utils/DicomFileUploader'; +import { Icon } from '@ohif/ui'; + +type DicomUploadProgressItemProps = { + dicomFileUploader: DicomFileUploader; +}; + +// eslint-disable-next-line react/display-name +const DicomUploadProgressItem = memo( + ({ dicomFileUploader }: DicomUploadProgressItemProps): ReactElement => { + const [percentComplete, setPercentComplete] = useState( + dicomFileUploader.getPercentComplete() + ); + const [failedReason, setFailedReason] = useState(''); + const [status, setStatus] = useState(dicomFileUploader.getStatus()); + + console.info(`${dicomFileUploader.getFileId()}`); + const isComplete = useCallback(() => { + return ( + status === UploadStatus.Failed || + status === UploadStatus.Cancelled || + status === UploadStatus.Success + ); + }, [status]); + + useEffect(() => { + const progressSubscription = dicomFileUploader.subscribe( + EVENTS.PROGRESS, + (dicomFileUploaderProgressEvent: DicomFileUploaderProgressEvent) => { + setPercentComplete(dicomFileUploaderProgressEvent.percentComplete); + } + ); + + dicomFileUploader + .load() + .catch((reason: UploadRejection) => { + setStatus(reason.status); + setFailedReason(reason.message ?? ''); + }) + .finally(() => setStatus(dicomFileUploader.getStatus())); + + return () => progressSubscription.unsubscribe(); + }, []); + + const cancelUpload = useCallback(() => { + dicomFileUploader.cancel(); + }, []); + + const getStatusIcon = (): ReactElement => { + switch (dicomFileUploader.getStatus()) { + case UploadStatus.Success: + return ( + + ); + case UploadStatus.InProgress: + return ; + case UploadStatus.Failed: + return ; + case UploadStatus.Cancelled: + return ; + default: + return <>; + } + }; + + return ( +
+
+
+
+ {getStatusIcon()} +
+
+ {dicomFileUploader.getFileName()} +
+
+ {failedReason &&
{failedReason}
} +
+
+ {!isComplete() && ( + <> + {dicomFileUploader.getStatus() === UploadStatus.InProgress && ( +
{percentComplete}%
+ )} +
+ +
+ + )} +
+
+ ); + } +); + +DicomUploadProgressItem.propTypes = { + dicomFileUploader: PropTypes.instanceOf(DicomFileUploader).isRequired, +}; + +export default DicomUploadProgressItem; diff --git a/extensions/cornerstone/src/getCustomizationModule.ts b/extensions/cornerstone/src/getCustomizationModule.ts index fa548b74a..acb064244 100644 --- a/extensions/cornerstone/src/getCustomizationModule.ts +++ b/extensions/cornerstone/src/getCustomizationModule.ts @@ -1,5 +1,6 @@ import { Enums } from '@cornerstonejs/tools'; import { toolNames } from './initCornerstoneTools'; +import DicomUpload from './components/DicomUpload/DicomUpload'; const tools = { active: [ @@ -22,6 +23,13 @@ const tools = { function getCustomizationModule() { return [ + { + name: 'cornerstoneDicomUploadComponent', + value: { + id: 'dicomUploadComponent', + component: DicomUpload, + }, + }, { name: 'default', value: [ diff --git a/extensions/cornerstone/src/utils/DicomFileUploader.ts b/extensions/cornerstone/src/utils/DicomFileUploader.ts new file mode 100644 index 000000000..64465e597 --- /dev/null +++ b/extensions/cornerstone/src/utils/DicomFileUploader.ts @@ -0,0 +1,220 @@ +import dicomImageLoader from '@cornerstonejs/dicom-image-loader'; + +import { PubSubService } from '@ohif/core'; + +export const EVENTS = { + PROGRESS: 'event:DicomFileUploader:progress', +}; + +export interface DicomFileUploaderEvent { + fileId: number; +} + +export interface DicomFileUploaderProgressEvent extends DicomFileUploaderEvent { + percentComplete: number; +} + +export enum UploadStatus { + NotStarted, + InProgress, + Success, + Failed, + Cancelled, +} + +type CancelOrFailed = UploadStatus.Cancelled | UploadStatus.Failed; + +export class UploadRejection { + message: string; + status: CancelOrFailed; + + constructor(status: CancelOrFailed, message: string) { + this.message = message; + this.status = status; + } +} + +export default class DicomFileUploader extends PubSubService { + private _file; + private _fileId; + private _dataSource; + private _loadPromise; + private _abortController = new AbortController(); + private _status: UploadStatus = UploadStatus.NotStarted; + private _percentComplete = 0; + + constructor(file, dataSource) { + super(EVENTS); + this._file = file; + this._fileId = dicomImageLoader.wadouri.fileManager.add(file); + this._dataSource = dataSource; + } + + getFileId(): string { + return this._fileId; + } + + getFileName(): string { + return this._file.name; + } + + getFileSize(): number { + return this._file.size; + } + + cancel(): void { + this._abortController.abort(); + } + + getStatus(): UploadStatus { + return this._status; + } + + getPercentComplete(): number { + return this._percentComplete; + } + + async load(): Promise { + if (this._loadPromise) { + // Already started loading, return the load promise. + return this._loadPromise; + } + + this._loadPromise = new Promise((resolve, reject) => { + // The upload listeners: fire progress events and/or settle the promise. + const uploadCallbacks = { + progress: evt => { + if (!evt.lengthComputable) { + // Progress computation is not possible. + return; + } + + this._status = UploadStatus.InProgress; + + this._percentComplete = Math.round((100 * evt.loaded) / evt.total); + this._broadcastEvent(EVENTS.PROGRESS, { + fileId: this._fileId, + percentComplete: this._percentComplete, + }); + }, + timeout: () => { + this._reject( + reject, + new UploadRejection(UploadStatus.Failed, 'The request timed out.') + ); + }, + abort: () => { + this._reject( + reject, + new UploadRejection(UploadStatus.Cancelled, 'Cancelled') + ); + }, + error: () => { + this._reject( + reject, + new UploadRejection(UploadStatus.Failed, 'The request failed.') + ); + }, + }; + + // First try to load the file. + dicomImageLoader.wadouri + .loadFileRequest(this._fileId) + .then(dicomFile => { + if (this._abortController.signal.aborted) { + this._reject( + reject, + new UploadRejection(UploadStatus.Cancelled, 'Cancelled') + ); + return; + } + + if (!this._checkDicomFile(dicomFile)) { + // The file is not DICOM + this._reject( + reject, + new UploadRejection( + UploadStatus.Failed, + 'Not a valid DICOM file.' + ) + ); + return; + } + + const request = new XMLHttpRequest(); + this._addRequestCallbacks(request, uploadCallbacks); + + // Do the actual upload by supplying the DICOM file and upload callbacks/listeners. + return this._dataSource.store + .dicom(dicomFile, request) + .then(() => { + this._status = UploadStatus.Success; + resolve(); + }) + .catch(reason => { + this._reject(reject, reason); + }); + }) + .catch(reason => { + this._reject(reject, reason); + }); + }); + + return this._loadPromise; + } + + private _isRejected(): boolean { + return ( + this._status === UploadStatus.Failed || + this._status === UploadStatus.Cancelled + ); + } + + private _reject(reject: (reason?: any) => void, reason: any) { + if (this._isRejected()) { + return; + } + + if (reason instanceof UploadRejection) { + this._status = reason.status; + reject(reason); + return; + } + + this._status = UploadStatus.Failed; + + if (reason.message) { + reject(new UploadRejection(UploadStatus.Failed, reason.message)); + return; + } + + reject(new UploadRejection(UploadStatus.Failed, reason)); + } + + private _addRequestCallbacks(request: XMLHttpRequest, uploadCallbacks) { + const abortCallback = () => request.abort(); + this._abortController.signal.addEventListener('abort', abortCallback); + + for (const [eventName, callback] of Object.entries(uploadCallbacks)) { + request.upload.addEventListener(eventName, callback); + } + + const cleanUpCallback = () => { + this._abortController.signal.removeEventListener('abort', abortCallback); + + for (const [eventName, callback] of Object.entries(uploadCallbacks)) { + request.upload.removeEventListener(eventName, callback); + } + + request.removeEventListener('loadend', cleanUpCallback); + }; + request.addEventListener('loadend', cleanUpCallback); + } + + private _checkDicomFile(arrayBuffer: ArrayBuffer) { + if (arrayBuffer.length <= 132) return false; + const arr = new Uint8Array(arrayBuffer.slice(128, 132)); + // bytes from 128 to 132 must be "DICM" + return Array.from('DICM').every((char, i) => char.charCodeAt(0) === arr[i]); + } +} diff --git a/extensions/default/package.json b/extensions/default/package.json index 81ca66393..958ebb288 100644 --- a/extensions/default/package.json +++ b/extensions/default/package.json @@ -33,7 +33,7 @@ "@ohif/core": "^3.0.0", "@ohif/i18n": "^1.0.0", "dcmjs": "^0.29.5", - "dicomweb-client": "^0.8.4", + "dicomweb-client": "^0.10.2", "prop-types": "^15.6.2", "react": "^17.0.2", "react-dom": "^17.0.2", diff --git a/extensions/default/src/DicomWebDataSource/index.js b/extensions/default/src/DicomWebDataSource/index.js index 792ee44c7..c5782375c 100644 --- a/extensions/default/src/DicomWebDataSource/index.js +++ b/extensions/default/src/DicomWebDataSource/index.js @@ -61,6 +61,8 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) { singlepart, } = dicomWebConfig; + const dicomWebConfigCopy = JSON.parse(JSON.stringify(dicomWebConfig)); + const qidoConfig = { url: qidoRoot, staticWado, @@ -230,36 +232,47 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) { }, store: { - dicom: async dataset => { + dicom: async (dataset, request) => { const headers = userAuthenticationService.getAuthorizationHeader(); if (headers) { wadoDicomWebClient.headers = headers; } - const meta = { - FileMetaInformationVersion: - dataset._meta.FileMetaInformationVersion.Value, - MediaStorageSOPClassUID: dataset.SOPClassUID, - MediaStorageSOPInstanceUID: dataset.SOPInstanceUID, - TransferSyntaxUID: EXPLICIT_VR_LITTLE_ENDIAN, - ImplementationClassUID, - ImplementationVersionName, - }; + if (dataset instanceof ArrayBuffer) { + const options = { + datasets: [dataset], + request, + }; - const denaturalized = denaturalizeDataset(meta); - const dicomDict = new DicomDict(denaturalized); + await wadoDicomWebClient.storeInstances(options); + } else { + const meta = { + FileMetaInformationVersion: + dataset._meta.FileMetaInformationVersion.Value, + MediaStorageSOPClassUID: dataset.SOPClassUID, + MediaStorageSOPInstanceUID: dataset.SOPInstanceUID, + TransferSyntaxUID: EXPLICIT_VR_LITTLE_ENDIAN, + ImplementationClassUID, + ImplementationVersionName, + }; - dicomDict.dict = denaturalizeDataset(dataset); + const denaturalized = denaturalizeDataset(meta); + const dicomDict = new DicomDict(denaturalized); - const part10Buffer = dicomDict.write(); + dicomDict.dict = denaturalizeDataset(dataset); - const options = { - datasets: [part10Buffer], - }; + const part10Buffer = dicomDict.write(); - await wadoDicomWebClient.storeInstances(options); + const options = { + datasets: [part10Buffer], + request, + }; + + await wadoDicomWebClient.storeInstances(options); + } }, }, + _retrieveSeriesMetadataSync: async ( StudyInstanceUID, filters, @@ -482,6 +495,9 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) { }); return imageIds; }, + getConfig() { + return dicomWebConfigCopy; + }, }; if (supportsReject) { diff --git a/platform/core/package.json b/platform/core/package.json index 1bfa7985f..43d410446 100644 --- a/platform/core/package.json +++ b/platform/core/package.json @@ -43,7 +43,7 @@ "dependencies": { "@babel/runtime": "^7.20.13", "dcmjs": "^0.29.5", - "dicomweb-client": "^0.8.4", + "dicomweb-client": "^0.10.2", "isomorphic-base64": "^1.0.2", "lodash.merge": "^4.6.1", "lodash.clonedeep": "^4.5.0", diff --git a/platform/core/src/DataSources/IWebApiDataSource.js b/platform/core/src/DataSources/IWebApiDataSource.js index 2cf785be3..a0b1a713f 100644 --- a/platform/core/src/DataSources/IWebApiDataSource.js +++ b/platform/core/src/DataSources/IWebApiDataSource.js @@ -21,6 +21,7 @@ function create({ deleteStudyMetadataPromise, getImageIdsForDisplaySet, getImageIdsForInstance, + getConfig, }) { const defaultQuery = { studies: { @@ -57,6 +58,11 @@ function create({ }; const defaultReject = {}; + + const defaultGetConfig = () => { + return { dicomUploadEnabled: false }; + }; + return { query: query || defaultQuery, retrieve: retrieve || defaultRetrieve, @@ -66,6 +72,7 @@ function create({ deleteStudyMetadataPromise, getImageIdsForDisplaySet, getImageIdsForInstance, + getConfig: getConfig || defaultGetConfig, }; } diff --git a/platform/ui/src/assets/icons/icon-alert-small.svg b/platform/ui/src/assets/icons/icon-alert-small.svg new file mode 100644 index 000000000..51151d709 --- /dev/null +++ b/platform/ui/src/assets/icons/icon-alert-small.svg @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/platform/ui/src/assets/icons/icon-status-alert.svg b/platform/ui/src/assets/icons/icon-status-alert.svg new file mode 100644 index 000000000..615d4a2fd --- /dev/null +++ b/platform/ui/src/assets/icons/icon-status-alert.svg @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/platform/ui/src/assets/icons/icon-transferring.svg b/platform/ui/src/assets/icons/icon-transferring.svg new file mode 100644 index 000000000..86379e138 --- /dev/null +++ b/platform/ui/src/assets/icons/icon-transferring.svg @@ -0,0 +1,6 @@ + + + + + + diff --git a/platform/ui/src/assets/icons/icon-upload.svg b/platform/ui/src/assets/icons/icon-upload.svg new file mode 100644 index 000000000..cdd1366fa --- /dev/null +++ b/platform/ui/src/assets/icons/icon-upload.svg @@ -0,0 +1,6 @@ + + + + + + diff --git a/platform/ui/src/assets/icons/icons-alert-outline.svg b/platform/ui/src/assets/icons/icons-alert-outline.svg new file mode 100644 index 000000000..747b65c78 --- /dev/null +++ b/platform/ui/src/assets/icons/icons-alert-outline.svg @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/platform/ui/src/components/Button/Button.tsx b/platform/ui/src/components/Button/Button.tsx index 939d803fd..8e8fcf7a2 100644 --- a/platform/ui/src/components/Button/Button.tsx +++ b/platform/ui/src/components/Button/Button.tsx @@ -58,6 +58,8 @@ const variants = { contained: { default: 'text-black hover:opacity-80 active:opacity-100 focus:opacity-80', primary: 'text-white hover:opacity-80 active:opacity-100 focus:opacity-80', + primaryDark: + 'text-primary-active hover:opacity-80 active:opacity-100 focus:opacity-80', secondary: 'text-white hover:opacity-80 active:opacity-100 focus:opacity-80', white: 'text-black hover:opacity-80 active:opacity-100 focus:opacity-80', @@ -93,6 +95,7 @@ const defaultVariantBackGroundColor = { contained: { default: 'bg-primary-light', primary: 'bg-primary-main', + primaryDark: 'bg-primary-dark', secondary: 'bg-secondary-light', white: 'bg-white', black: 'bg-black', @@ -231,6 +234,7 @@ Button.propTypes = { color: PropTypes.oneOf([ 'default', 'primary', + 'primaryDark', 'primaryActive', 'secondary', 'white', diff --git a/platform/ui/src/components/Icon/getIcon.js b/platform/ui/src/components/Icon/getIcon.js index 3627697af..103bcef9e 100644 --- a/platform/ui/src/components/Icon/getIcon.js +++ b/platform/ui/src/components/Icon/getIcon.js @@ -50,6 +50,8 @@ import tracked from './../../assets/icons/tracked.svg'; import unlink from './../../assets/icons/unlink.svg'; import checkboxChecked from './../../assets/icons/checkbox-checked.svg'; import checkboxUnchecked from './../../assets/icons/checkbox-unchecked.svg'; +import iconAlertOutline from './../../assets/icons/icons-alert-outline.svg'; +import iconAlertSmall from './../../assets/icons/icon-alert-small.svg'; import iconClose from './../../assets/icons/icon-close.svg'; import iconNextInactive from './../../assets/icons/icon-next-inactive.svg'; import iconNext from './../../assets/icons/icon-next.svg'; @@ -57,6 +59,9 @@ import iconPlay from './../../assets/icons/icon-play.svg'; import iconPause from './../../assets/icons/icon-pause.svg'; import iconPrevInactive from './../../assets/icons/icon-prev-inactive.svg'; import iconPrev from './../../assets/icons/icon-prev.svg'; +import iconStatusAlert from './../../assets/icons/icon-status-alert.svg'; +import iconTransferring from './../../assets/icons/icon-transferring.svg'; +import iconUpload from './../../assets/icons/icon-upload.svg'; import navigationPanelRightHide from './../../assets/icons/navigation-panel-right-hide.svg'; import navigationPanelRightReveal from './../../assets/icons/navigation-panel-right-reveal.svg'; import tabLinear from './../../assets/icons/tab-linear.svg'; @@ -144,9 +149,13 @@ const ICONS = { 'external-link': externalLink, 'group-layers': groupLayers, info: info, + 'icon-alert-outline': iconAlertOutline, + 'icon-alert-small': iconAlertSmall, 'icon-close': iconClose, 'icon-play': iconPlay, 'icon-pause': iconPause, + 'icon-status-alert': iconStatusAlert, + 'icon-transferring': iconTransferring, 'info-action': infoAction, 'info-link': infoLink, 'arrow-left': arrowLeft, @@ -230,6 +239,7 @@ const ICONS = { 'icon-next': iconNext, 'icon-prev-inactive': iconPrevInactive, 'icon-prev': iconPrev, + 'icon-upload': iconUpload, 'navigation-panel-right-hide': navigationPanelRightHide, 'navigation-panel-right-reveal': navigationPanelRightReveal, 'tab-linear': tabLinear, diff --git a/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.tsx b/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.tsx index 78376bd83..2c18a8bf4 100644 --- a/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.tsx +++ b/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.tsx @@ -1,8 +1,7 @@ import React from 'react'; import classNames from 'classnames'; import { Icon } from '@ohif/ui'; - -import './LoadingIndicatorProgress.css'; +import ProgressLoadingBar from '../ProgressLoadingBar'; /** * A React component that renders a loading indicator. @@ -19,18 +18,8 @@ function LoadingIndicatorProgress({ className, textBlock, progress }) { )} > -
- {progress === undefined || progress === null ? ( -
- ) : ( -
- )} +
+
{textBlock}
diff --git a/platform/ui/src/components/Modal/Modal.tsx b/platform/ui/src/components/Modal/Modal.tsx index 7d0d9e67e..0aa409f49 100644 --- a/platform/ui/src/components/Modal/Modal.tsx +++ b/platform/ui/src/components/Modal/Modal.tsx @@ -18,6 +18,7 @@ const Modal = ({ title, onClose, children, + shouldCloseOnOverlayClick, }) => { const { hide } = useModal(); @@ -56,6 +57,7 @@ const Modal = ({ onRequestClose={handleClose} isOpen={isOpen} title={title} + shouldCloseOnOverlayClick={shouldCloseOnOverlayClick} > {renderHeader()}
@@ -67,6 +69,7 @@ const Modal = ({ Modal.defaultProps = { shouldCloseOnEsc: true, + shouldCloseOnOverlayClick: true, }; Modal.propTypes = { @@ -80,6 +83,7 @@ Modal.propTypes = { PropTypes.arrayOf(PropTypes.node), PropTypes.node, ]).isRequired, + shouldCloseOnOverlayClick: PropTypes.bool, }; export default Modal; diff --git a/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.css b/platform/ui/src/components/ProgressLoadingBar/ProgressLoadingBar.css similarity index 71% rename from platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.css rename to platform/ui/src/components/ProgressLoadingBar/ProgressLoadingBar.css index b07886041..f9addbe9e 100644 --- a/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.css +++ b/platform/ui/src/components/ProgressLoadingBar/ProgressLoadingBar.css @@ -4,7 +4,7 @@ border-radius: 4px; overflow: hidden; position: relative; - width: 12em; + width: 100%; } .infinite-loading-bar { @@ -15,14 +15,6 @@ width: 50%; } -.loading-bar { - animation: side2side 2s ease-in-out infinite; - height: 100%; - border-radius: 4px; - position: absolute; - width: 50%; -} - @keyframes side2side { 0%, 100% { diff --git a/platform/ui/src/components/ProgressLoadingBar/ProgressLoadingBar.tsx b/platform/ui/src/components/ProgressLoadingBar/ProgressLoadingBar.tsx new file mode 100644 index 000000000..e5807b4f7 --- /dev/null +++ b/platform/ui/src/components/ProgressLoadingBar/ProgressLoadingBar.tsx @@ -0,0 +1,34 @@ +import React, { ReactElement } from 'react'; + +import './ProgressLoadingBar.css'; + +export type ProgressLoadingBarProps = { + progress?: number; +}; +/** + * A React component that renders a loading progress bar. + * If progress is not provided, it will render an infinite loading bar + * If progress is provided, it will render a progress bar + * The progress text can be optionally displayed to the left of the bar. + */ +function ProgressLoadingBar({ + progress, +}: ProgressLoadingBarProps): ReactElement { + return ( +
+ {progress === undefined || progress === null ? ( +
+ ) : ( +
+ )} +
+ ); +} + +export default ProgressLoadingBar; diff --git a/platform/ui/src/components/ProgressLoadingBar/index.js b/platform/ui/src/components/ProgressLoadingBar/index.js new file mode 100644 index 000000000..ab8869ffc --- /dev/null +++ b/platform/ui/src/components/ProgressLoadingBar/index.js @@ -0,0 +1,2 @@ +import ProgressLoadingBar from './ProgressLoadingBar'; +export default ProgressLoadingBar; diff --git a/platform/ui/src/components/StudyListFilter/StudyListFilter.tsx b/platform/ui/src/components/StudyListFilter/StudyListFilter.tsx index 1e8008c80..a266c00dc 100644 --- a/platform/ui/src/components/StudyListFilter/StudyListFilter.tsx +++ b/platform/ui/src/components/StudyListFilter/StudyListFilter.tsx @@ -11,6 +11,7 @@ const StudyListFilter = ({ clearFilters, isFiltering, numOfStudies, + onUploadClick, }) => { const { t } = useTranslation('StudyList'); const { sortBy, sortDirection } = filterValues; @@ -33,6 +34,15 @@ const StudyListFilter = ({ {t('StudyList')} + {onUploadClick && ( +
+ + Upload +
+ )}
{isFiltering && ( @@ -119,6 +129,7 @@ StudyListFilter.propTypes = { onChange: PropTypes.func.isRequired, clearFilters: PropTypes.func.isRequired, isFiltering: PropTypes.bool.isRequired, + onUploadClick: PropTypes.func, }; export default StudyListFilter; diff --git a/platform/ui/src/components/index.js b/platform/ui/src/components/index.js index d01247542..4ca26c7e2 100644 --- a/platform/ui/src/components/index.js +++ b/platform/ui/src/components/index.js @@ -70,6 +70,7 @@ import CheckBox from './CheckBox'; import LoadingIndicatorProgress from './LoadingIndicatorProgress'; import LoadingIndicatorTotalPercent from './LoadingIndicatorTotalPercent'; import ViewportActionBar from './ViewportActionBar'; +import ProgressLoadingBar from './ProgressLoadingBar'; export { AboutModal, @@ -110,6 +111,7 @@ export { Modal, NavBar, Notification, + ProgressLoadingBar, Select, SegmentationTable, SegmentationGroupTable, diff --git a/platform/ui/src/contextProviders/ModalProvider.tsx b/platform/ui/src/contextProviders/ModalProvider.tsx index 382b8a242..85902df2f 100644 --- a/platform/ui/src/contextProviders/ModalProvider.tsx +++ b/platform/ui/src/contextProviders/ModalProvider.tsx @@ -32,6 +32,7 @@ const ModalProvider = ({ children, modal: Modal, service }) => { content: null, contentProps: null, shouldCloseOnEsc: true, + shouldCloseOnOverlayClick: true, isOpen: true, closeButton: true, title: null, @@ -39,7 +40,6 @@ const ModalProvider = ({ children, modal: Modal, service }) => { }; const { t } = useTranslation('Modals'); - const [options, setOptions] = useState(DEFAULT_OPTIONS); /** @@ -57,9 +57,9 @@ const ModalProvider = ({ children, modal: Modal, service }) => { * * @returns void */ - const hide = useCallback(() => setOptions(DEFAULT_OPTIONS), [ - DEFAULT_OPTIONS, - ]); + const hide = useCallback(() => { + setOptions(DEFAULT_OPTIONS); + }, [DEFAULT_OPTIONS]); /** * Sets the implementation of a modal service that can be used by extensions. @@ -80,6 +80,7 @@ const ModalProvider = ({ children, modal: Modal, service }) => { customClassName, shouldCloseOnEsc, closeButton, + shouldCloseOnOverlayClick, } = options; return ( @@ -92,6 +93,7 @@ const ModalProvider = ({ children, modal: Modal, service }) => { title={t(title)} closeButton={closeButton} onClose={hide} + shouldCloseOnOverlayClick={shouldCloseOnOverlayClick} > diff --git a/platform/ui/src/index.js b/platform/ui/src/index.js index fad709a2c..7b51fd785 100644 --- a/platform/ui/src/index.js +++ b/platform/ui/src/index.js @@ -70,6 +70,7 @@ export { Modal, NavBar, Notification, + ProgressLoadingBar, Select, SegmentationTable, SegmentationGroupTable, diff --git a/platform/viewer/public/config/local_dcm4chee.js b/platform/viewer/public/config/local_dcm4chee.js index fca1f2a71..44dbba9d3 100644 --- a/platform/viewer/public/config/local_dcm4chee.js +++ b/platform/viewer/public/config/local_dcm4chee.js @@ -1,5 +1,9 @@ window.config = { routerBasename: '/', + customizationService: { + dicomUploadComponent: + '@ohif/extension-cornerstone.customizationModule.cornerstoneDicomUploadComponent', + }, showStudyList: true, extensions: [], modes: [], @@ -26,6 +30,7 @@ window.config = { requestOptions: { auth: 'admin:admin', }, + dicomUploadEnabled: true, }, }, { diff --git a/platform/viewer/public/config/local_orthanc.js b/platform/viewer/public/config/local_orthanc.js index 71bacacbe..9b5d086b6 100644 --- a/platform/viewer/public/config/local_orthanc.js +++ b/platform/viewer/public/config/local_orthanc.js @@ -3,6 +3,10 @@ window.config = { // whiteLabelling: {}, extensions: [], modes: [], + customizationService: { + dicomUploadComponent: + '@ohif/extension-cornerstone.customizationModule.cornerstoneDicomUploadComponent', + }, showStudyList: true, maxNumberOfWebWorkers: 3, showLoadingIndicator: true, @@ -28,6 +32,7 @@ window.config = { useBulkDataURI: false, supportsFuzzyMatching: true, supportsWildcard: true, + dicomUploadEnabled: true, }, }, { diff --git a/platform/viewer/src/routes/DataSourceWrapper.tsx b/platform/viewer/src/routes/DataSourceWrapper.tsx index 51fa05d95..d5357875e 100644 --- a/platform/viewer/src/routes/DataSourceWrapper.tsx +++ b/platform/viewer/src/routes/DataSourceWrapper.tsx @@ -56,13 +56,14 @@ function DataSourceWrapper(props) { // But only for LayoutTemplate type of 'list'? // Or no data fetching here, and just hand down my source const STUDIES_LIMIT = 101; - const [data, setData] = useState({ + const DEFAULT_DATA = { studies: [], total: 0, resultsPerPage: 25, pageNumber: 1, location: 'Not a valid location, causes first load to occur', - }); + }; + const [data, setData] = useState(DEFAULT_DATA); const [isLoading, setIsLoading] = useState(false); useEffect(() => { @@ -125,6 +126,8 @@ function DataSourceWrapper(props) { dataTotal={data.total} dataSource={dataSource} isLoadingData={isLoading} + // To refresh the data, simply reset it to DEFAULT_DATA which invalidates it and triggers a new query to fetch the data. + onRefresh={() => setData(DEFAULT_DATA)} /> ); } diff --git a/platform/viewer/src/routes/WorkList/WorkList.tsx b/platform/viewer/src/routes/WorkList/WorkList.tsx index e2e1fde2c..52d8928ca 100644 --- a/platform/viewer/src/routes/WorkList/WorkList.tsx +++ b/platform/viewer/src/routes/WorkList/WorkList.tsx @@ -10,7 +10,7 @@ import { useTranslation } from 'react-i18next'; import filtersMeta from './filtersMeta.js'; import { useAppConfig } from '@state'; import { useDebounce, useSearchParams } from '@hooks'; -import { utils, hotkeys } from '@ohif/core'; +import { utils, hotkeys, ServicesManager } from '@ohif/core'; import { Icon, @@ -47,6 +47,8 @@ function WorkList({ dataSource, hotkeysManager, dataPath, + onRefresh, + servicesManager, }) { const { hotkeyDefinitions, hotkeyDefaults } = hotkeysManager; const { show, hide } = useModal(); @@ -429,6 +431,33 @@ function WorkList({ }); } + const { customizationService } = servicesManager.services; + const { component: dicomUploadComponent } = + customizationService.get('dicomUploadComponent') ?? {}; + const uploadProps = + dicomUploadComponent && dataSource.getConfig().dicomUploadEnabled + ? { + title: 'Upload files', + closeButton: true, + shouldCloseOnEsc: false, + shouldCloseOnOverlayClick: false, + content: dicomUploadComponent.bind(null, { + dataSource, + onComplete: () => { + hide(); + onRefresh(); + }, + onStarted: () => { + show({ + ...uploadProps, + // when upload starts, hide the default close button as closing the dialogue must be handled by the upload dialogue itself + closeButton: false, + }); + }, + }), + } + : undefined; + return (
setFilterValues(defaultFilterValues)} isFiltering={isFiltering(filterValues, defaultFilterValues)} + onUploadClick={uploadProps ? () => show(uploadProps) : undefined} /> {hasStudies ? ( <> @@ -478,8 +508,10 @@ WorkList.propTypes = { data: PropTypes.array.isRequired, dataSource: PropTypes.shape({ query: PropTypes.object.isRequired, + getConfig: PropTypes.func, }).isRequired, isLoadingData: PropTypes.bool.isRequired, + servicesManager: PropTypes.instanceOf(ServicesManager), }; const defaultFilterValues = { diff --git a/platform/viewer/src/routes/index.tsx b/platform/viewer/src/routes/index.tsx index ab5a605a5..90162b2a4 100644 --- a/platform/viewer/src/routes/index.tsx +++ b/platform/viewer/src/routes/index.tsx @@ -25,12 +25,6 @@ const bakedInRoutes = [ // NOT FOUND (404) const notFoundRoute = { component: NotFound }; -const WorkListRoute = { - path: '/', - children: DataSourceWrapper, - private: true, - props: { children: WorkList }, -}; const createRoutes = ({ modes, @@ -54,6 +48,13 @@ const createRoutes = ({ const { customizationService } = servicesManager.services; + const WorkListRoute = { + path: '/', + children: DataSourceWrapper, + private: true, + props: { children: WorkList, servicesManager }, + }; + const customRoutes = customizationService.getGlobalCustomization( 'customRoutes' ); diff --git a/yarn.lock b/yarn.lock index e4f3f7807..d8eda8ae3 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1272,7 +1272,7 @@ core-js-pure "^3.25.1" regenerator-runtime "^0.13.11" -"@babel/runtime@7.17.9", "@babel/runtime@7.7.6", "@babel/runtime@^7.1.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.14.6", "@babel/runtime@^7.17.8", "@babel/runtime@^7.18.6", "@babel/runtime@^7.20.13", "@babel/runtime@^7.20.7", "@babel/runtime@^7.21.0", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.2", "@babel/runtime@^7.7.4", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.9.2": +"@babel/runtime@7.17.9", "@babel/runtime@7.7.6", "@babel/runtime@^7.1.2", "@babel/runtime@^7.10.3", "@babel/runtime@^7.11.2", "@babel/runtime@^7.12.13", "@babel/runtime@^7.12.5", "@babel/runtime@^7.14.6", "@babel/runtime@^7.17.8", "@babel/runtime@^7.18.6", "@babel/runtime@^7.20.13", "@babel/runtime@^7.20.7", "@babel/runtime@^7.3.1", "@babel/runtime@^7.4.4", "@babel/runtime@^7.4.5", "@babel/runtime@^7.5.5", "@babel/runtime@^7.7.2", "@babel/runtime@^7.7.4", "@babel/runtime@^7.7.6", "@babel/runtime@^7.8.4", "@babel/runtime@^7.9.2": version "7.21.0" resolved "https://registry.npmjs.org/@babel/runtime/-/runtime-7.21.0.tgz#5b55c9d394e5fcf304909a8b00c07dc217b56673" integrity sha512-xwII0//EObnq89Ji5AKYQaRYiW/nZ3llSv29d49IuxPhKbtJoLP+9QUUZ4nVragQVtaVGeZrpB+ZtG/Pdy/POw== @@ -1387,34 +1387,19 @@ resolved "https://registry.npmjs.org/@cornerstonejs/calculate-suv/-/calculate-suv-1.0.3.tgz#6d99a72032c0f90cebf44dc6f0b12a5f1102e884" integrity sha512-2SwVJKzC1DzyxdxJtCht9dhTND2GFjLwhhkDyyC7vJq5tIgbhxgPk1CSwovO1pxmoybAXzjOxnaubllxLgoT+w== -"@cornerstonejs/codec-charls@^0.1.1": - 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version "0.3.2" - resolved "https://registry.yarnpkg.com/sort-object/-/sort-object-0.3.2.tgz#98e0d199ede40e07c61a84403c61d6c3b290f9e2" - integrity sha512-aAQiEdqFTTdsvUFxXm3umdo04J7MRljoVGbBlkH7BgNsMvVNAJyGj7C/wV1A8wHWAJj/YikeZbfuCKqhggNWGA== - dependencies: - sort-asc "^0.1.0" - sort-desc "^0.1.1" - source-list-map@^2.0.0: version "2.0.1" resolved "https://registry.npmjs.org/source-list-map/-/source-list-map-2.0.1.tgz#3993bd873bfc48479cca9ea3a547835c7c154b34" @@ -21086,11 +20823,6 @@ timsort@^0.3.0: resolved "https://registry.npmjs.org/timsort/-/timsort-0.3.0.tgz#405411a8e7e6339fe64db9a234de11dc31e02bd4" integrity sha512-qsdtZH+vMoCARQtyod4imc2nIJwg9Cc7lPRrw9CzF8ZKR0khdr8+2nX80PBhET3tcyTtJDxAffGh2rXH4tyU8A== -tiny-emitter@^2.1.0: - version "2.1.0" - resolved "https://registry.yarnpkg.com/tiny-emitter/-/tiny-emitter-2.1.0.tgz#1d1a56edfc51c43e863cbb5382a72330e3555423" - integrity sha512-NB6Dk1A9xgQPMoGqC5CVXn123gWyte215ONT5Pp5a0yt4nlEoO1ZWeCwpncaekPHXO60i47ihFnZPiRPjRMq4Q== - tiny-invariant@^1.0.2: version "1.3.1" resolved "https://registry.npmjs.org/tiny-invariant/-/tiny-invariant-1.3.1.tgz#8560808c916ef02ecfd55e66090df23a4b7aa642" @@ -21352,11 +21084,6 @@ typed-array-length@^1.0.4: for-each "^0.3.3" is-typed-array "^1.1.9" -typed-function@^4.1.0: - version "4.1.0" - resolved "https://registry.npmjs.org/typed-function/-/typed-function-4.1.0.tgz#da4bdd8a6d19a89e22732f75e4a410860aaf9712" - integrity sha512-DGwUl6cioBW5gw2L+6SMupGwH/kZOqivy17E4nsh1JI9fKF87orMmlQx3KISQPmg3sfnOUGlwVkroosvgddrlg== - typedarray-to-buffer@^3.1.5: version "3.1.5" resolved "https://registry.npmjs.org/typedarray-to-buffer/-/typedarray-to-buffer-3.1.5.tgz#a97ee7a9ff42691b9f783ff1bc5112fe3fca9080" @@ -21853,7 +21580,7 @@ uuid@^8.3.2: resolved "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz#80d5b5ced271bb9af6c445f21a1a04c606cefbe2" integrity sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg== -uuid@^9.0, uuid@^9.0.0: +uuid@^9.0.0: version "9.0.0" resolved "https://registry.npmjs.org/uuid/-/uuid-9.0.0.tgz#592f550650024a38ceb0c562f2f6aa435761efb5" integrity sha512-MXcSTerfPa4uqyzStbRoTgt5XIe3x5+42+q1sDuy3R5MDk66URdLMOZe5aPX/SQd+kuYAh0FdP/pO28IkQyTeg== @@ -22052,11 +21779,6 @@ web-streams-polyfill@^3.0.3: resolved "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.2.1.tgz#71c2718c52b45fd49dbeee88634b3a60ceab42a6" integrity sha512-e0MO3wdXWKrLbL0DgGnUV7WHVuw9OUvL4hjgnPkIeEvESk74gAITi5G606JtZPp39cd8HA9VQzCIvA49LpPN5Q== -web-worker@^1.2.0: - version "1.2.0" - resolved "https://registry.yarnpkg.com/web-worker/-/web-worker-1.2.0.tgz#5d85a04a7fbc1e7db58f66595d7a3ac7c9c180da" - integrity sha512-PgF341avzqyx60neE9DD+XS26MMNMoUQRz9NOZwW32nPQrF6p77f1htcnjBSEV8BGMKZ16choqUG4hyI0Hx7mA== - webgl-constants@^1.1.1: version "1.1.1" resolved "https://registry.npmjs.org/webgl-constants/-/webgl-constants-1.1.1.tgz#f9633ee87fea56647a60b9ce735cbdfb891c6855" @@ -22777,11 +22499,6 @@ xml-name-validator@^3.0.0: resolved "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-3.0.0.tgz#6ae73e06de4d8c6e47f9fb181f78d648ad457c6a" integrity sha512-A5CUptxDsvxKJEU3yO6DuWBSJz/qizqzJKOMIfUJHETbBw/sFaDxgd6fxm1ewUaM0jZ444Fc5vC5ROYurg/4Pw== -xml-utils@^1.0.2: - version "1.3.0" - resolved "https://registry.yarnpkg.com/xml-utils/-/xml-utils-1.3.0.tgz#f1043534e3ac3deda12ddab39f8442e16da98ebb" - integrity sha512-i4PIrX33Wd66dvwo4syicwlwmnr6wuvvn4f2ku9hA67C2Uk62Xubczuhct+Evnd12/DV71qKNeDdJwES8HX1RA== - xml@^1.0.1: version "1.0.1" resolved "https://registry.npmjs.org/xml/-/xml-1.0.1.tgz#78ba72020029c5bc87b8a81a3cfcd74b4a2fc1e5" From b5b936b53e561191afa59fed803009040afc391f Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 1 May 2023 12:54:33 -0400 Subject: [PATCH 23/54] fix(jump): Jump to measurement wasn't jumping when presentation already existed (#3318) * fix: Jump to measurement after presentation store * Fix initial load of DICOM SR * Fix measurement highlight issues * Clear measurements changed to array * Fix merge issues * PR comments * Removed unused formatting. Change to single event * Fix the unit test * PR review comments * refactor(viewport): simplify imports, align destructuring Simplify import statements by removing unused imports, organize existing imports, and align destructured imports consistently across the component. --------- --- .../utils/createReferencedImageDisplaySet.ts | 10 +- .../viewports/OHIFCornerstoneSRViewport.tsx | 13 +- .../src/Viewport/OHIFCornerstoneViewport.tsx | 84 +++-- extensions/cornerstone/src/commandsModule.ts | 109 ++----- .../CornerstoneCacheService.ts | 15 +- .../CornerstoneViewportService.ts | 28 ++ .../src/services/ViewportService/Viewport.ts | 29 ++ .../src/types/CornerstoneCacheService.ts | 21 +- .../measurementServiceMappings/Length.ts | 1 + extensions/default/src/commandsModule.ts | 8 +- .../TrackedMeasurementsContext.tsx | 9 + .../MeasurementService/MeasurementService.ts | 101 +++--- .../ViewportGridService.ts | 49 ++- .../getPresentationIds.ts | 1 + .../_shared/pubSubServiceInterface.js | 16 + platform/core/src/utils/absoluteUrl.test.js | 23 +- .../services/data/MeasurementService.md | 3 +- .../contextProviders/ViewportGridProvider.tsx | 22 +- platform/ui/src/types/index.ts | 2 +- .../viewer/src/components/ViewportGrid.tsx | 96 ++---- yarn.lock | 298 +++++++++++++++++- 21 files changed, 640 insertions(+), 298 deletions(-) rename platform/{ui/src/contextProviders => core/src/services/ViewportGridService}/getPresentationIds.ts (99%) diff --git a/extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts b/extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts index 0abff2b3c..03744c26d 100644 --- a/extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts +++ b/extensions/cornerstone-dicom-sr/src/utils/createReferencedImageDisplaySet.ts @@ -3,10 +3,8 @@ import { DisplaySetService, classes } from '@ohif/core'; const ImageSet = classes.ImageSet; const findInstance = (measurement, displaySetService: DisplaySetService) => { - const { - displaySetInstanceUID, - ReferencedSOPInstanceUID: sopUid, - } = measurement; + const { displaySetInstanceUID, ReferencedSOPInstanceUID: sopUid } = + measurement; const referencedDisplaySet = displaySetService.getDisplaySetByUID( displaySetInstanceUID ); @@ -52,7 +50,7 @@ const findReferencedInstances = ( const createReferencedImageDisplaySet = (displaySetService, displaySet) => { const instances = findReferencedInstances(displaySetService, displaySet); // This will be a member function of the created image set - const updateInstances = function() { + const updateInstances = function () { this.images.splice( 0, this.images.length, @@ -77,6 +75,8 @@ const createReferencedImageDisplaySet = (displaySetService, displaySet) => { numImageFrames: instances.length, SOPClassHandlerId: `@ohif/extension-default.sopClassHandlerModule.stack`, isReconstructable: false, + // This object is made of multiple instances from other series + isCompositeStack: true, madeInClient: true, updateInstances, }); diff --git a/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx b/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx index 4ef8f2bdf..0223ffbc9 100644 --- a/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx +++ b/extensions/cornerstone-dicom-sr/src/viewports/OHIFCornerstoneSRViewport.tsx @@ -2,18 +2,10 @@ import PropTypes from 'prop-types'; import React, { useCallback, useContext, useEffect, useState } from 'react'; import { useTranslation } from 'react-i18next'; import OHIF, { utils, ServicesManager, ExtensionManager } from '@ohif/core'; -import { CornerstoneServices } from '@ohif/extension-cornerstone/types'; import { setTrackingUniqueIdentifiersForElement } from '../tools/modules/dicomSRModule'; -import { - Icon, - Notification, - Tooltip, - useViewportDialog, - useViewportGrid, - ViewportActionBar, -} from '@ohif/ui'; +import { Icon, Tooltip, useViewportGrid, ViewportActionBar } from '@ohif/ui'; import hydrateStructuredReport from '../utils/hydrateStructuredReport'; import createReferencedImageDisplaySet from '../utils/createReferencedImageDisplaySet'; @@ -40,7 +32,7 @@ function OHIFCornerstoneSRViewport(props) { displaySetService, cornerstoneViewportService, measurementService, - } = servicesManager.services as CornerstoneServices; + } = servicesManager.services; // SR viewport will always have a single display set if (displaySets.length > 1) { @@ -50,7 +42,6 @@ function OHIFCornerstoneSRViewport(props) { const srDisplaySet = displaySets[0]; const [viewportGrid, viewportGridService] = useViewportGrid(); - const [viewportDialogState, viewportDialogApi] = useViewportDialog(); const [measurementSelected, setMeasurementSelected] = useState(0); const [measurementCount, setMeasurementCount] = useState(1); const [activeImageDisplaySetData, setActiveImageDisplaySetData] = useState( diff --git a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx index 1071814bc..a55d74edd 100644 --- a/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx +++ b/extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx @@ -9,6 +9,7 @@ import { StackViewport, utilities as csUtils, } from '@cornerstonejs/core'; +import { MeasurementService } from '@ohif/core'; import { CinePlayer, useCine, @@ -30,6 +31,12 @@ import CornerstoneServices from '../types/CornerstoneServices'; const STACK = 'stack'; +/** + * Caches the jump to measurement operation, so that if display set is shown, + * it can jump to the measurement. + */ +let cacheJumpToMeasurementEvent; + function areEqual(prevProps, nextProps) { if (nextProps.needsRerendering) { return false; @@ -412,6 +419,13 @@ const OHIFCornerstoneViewport = React.memo(props => { lutPresentation: lutPresentationStore[presentationIds?.lutPresentationId], }; + let measurement; + if (cacheJumpToMeasurementEvent?.viewportIndex === viewportIndex) { + measurement = cacheJumpToMeasurementEvent.measurement; + // Delete the position presentation so that viewport navigates direct + presentations.positionPresentation = null; + cacheJumpToMeasurementEvent = null; + } cornerstoneViewportService.setViewportData( viewportIndex, @@ -420,6 +434,10 @@ const OHIFCornerstoneViewport = React.memo(props => { displaySetOptions, presentations ); + + if (measurement) { + cs3DTools.annotation.selection.setAnnotationSelected(measurement.uid); + } }; loadViewportData(); @@ -536,22 +554,30 @@ function _subscribeToJumpToMeasurementEvents( displaySet => displaySet.displaySetInstanceUID ); const { unsubscribe } = measurementService.subscribe( - measurementService.EVENTS.JUMP_TO_MEASUREMENT, - ({ measurement }) => { - if (!measurement) return; - - // Jump the the measurement if the viewport contains the displaySetUID (fusion) - if (displaysUIDs.includes(measurement.displaySetInstanceUID)) { - _jumpToMeasurement( - measurement, - elementRef, - viewportIndex, - measurementService, - displaySetService, - viewportGridService, - cornerstoneViewportService + MeasurementService.EVENTS.JUMP_TO_MEASUREMENT_VIEWPORT, + props => { + cacheJumpToMeasurementEvent = props; + const { viewportIndex: jumpIndex, measurement, isConsumed } = props; + if (!measurement || isConsumed) return; + if (cacheJumpToMeasurementEvent.cornerstoneViewport === undefined) { + // Decide on which viewport should handle this + cacheJumpToMeasurementEvent.cornerstoneViewport = cornerstoneViewportService.getViewportIndexToJump( + jumpIndex, + measurement.displaySetInstanceUID, + { referencedImageId: measurement.referencedImageId } ); } + if (cacheJumpToMeasurementEvent.cornerstoneViewport !== viewportIndex) + return; + _jumpToMeasurement( + measurement, + elementRef, + viewportIndex, + measurementService, + displaySetService, + viewportGridService, + cornerstoneViewportService + ); } ); @@ -568,21 +594,19 @@ function _checkForCachedJumpToMeasurementEvents( viewportGridService, cornerstoneViewportService ) { + if (!cacheJumpToMeasurementEvent) return; + if (cacheJumpToMeasurementEvent.isConsumed) { + cacheJumpToMeasurementEvent = null; + return; + } const displaysUIDs = displaySets.map( displaySet => displaySet.displaySetInstanceUID ); if (!displaysUIDs?.length) return; - const measurementIdToJumpTo = measurementService.getJumpToMeasurement( - viewportIndex - ); - - if (measurementIdToJumpTo && elementRef) { - // Jump to measurement if the measurement exists - const measurement = measurementService.getMeasurement( - measurementIdToJumpTo - ); - + // Jump to measurement if the measurement exists + const { measurement } = cacheJumpToMeasurementEvent; + if (measurement && elementRef) { if (displaysUIDs.includes(measurement?.displaySetInstanceUID)) { _jumpToMeasurement( measurement, @@ -611,6 +635,7 @@ function _jumpToMeasurement( if (!SOPInstanceUID) { console.warn('cannot jump in a non-acquisition plane measurements yet'); + return; } const referencedDisplaySet = displaySetService.getDisplaySetByUID( @@ -623,15 +648,17 @@ function _jumpToMeasurement( viewportGridService.setActiveViewportIndex(viewportIndex); - const enableElement = getEnabledElement(targetElement); + const enabledElement = getEnabledElement(targetElement); const viewportInfo = cornerstoneViewportService.getViewportInfoByIndex( viewportIndex ); - if (enableElement) { + if (enabledElement) { // See how the jumpToSlice() of Cornerstone3D deals with imageIdx param. - const viewport = enableElement.viewport as IStackViewport | IVolumeViewport; + const viewport = enabledElement.viewport as + | IStackViewport + | IVolumeViewport; let imageIdIndex = 0; let viewportCameraDirectionMatch = true; @@ -680,7 +707,8 @@ function _jumpToMeasurement( cs3DTools.annotation.selection.setAnnotationSelected(measurement.uid); // Jump to measurement consumed, remove. - measurementService.removeJumpToMeasurement(viewportIndex); + cacheJumpToMeasurementEvent?.consume?.(); + cacheJumpToMeasurementEvent = null; } } diff --git a/extensions/cornerstone/src/commandsModule.ts b/extensions/cornerstone/src/commandsModule.ts index c57d3b0a9..beb45115d 100644 --- a/extensions/cornerstone/src/commandsModule.ts +++ b/extensions/cornerstone/src/commandsModule.ts @@ -10,6 +10,7 @@ import { utilities as cstUtils, ReferenceLinesTool, } from '@cornerstonejs/tools'; +import { Types as OhifTypes } from '@ohif/core'; import CornerstoneViewportDownloadForm from './utils/CornerstoneViewportDownloadForm'; import callInputDialog from './utils/callInputDialog'; @@ -19,7 +20,10 @@ import { getFirstAnnotationSelected } from './utils/measurementServiceMappings/u import getActiveViewportEnabledElement from './utils/getActiveViewportEnabledElement'; import { CornerstoneServices } from './types'; -function commandsModule({ servicesManager, commandsManager }) { +function commandsModule({ + servicesManager, + commandsManager, +}: OhifTypes.Extensions.ExtensionParams): OhifTypes.Extensions.CommandsModule { const { viewportGridService, toolGroupService, @@ -484,33 +488,22 @@ function commandsModule({ servicesManager, commandsManager }) { } } }, - firstImage: () => { - // Get current active viewport (return if none active) - const enabledElement = _getActiveViewportEnabledElement(); - if (!enabledElement) { - return; - } - const { viewport } = enabledElement; - // Check viewport is supported - if ( - viewport! instanceof StackViewport && - viewport! instanceof VolumeViewport - ) { - throw new Error('Unsupported viewport type'); - } - - // Set slice to first slice - const options = { imageIndex: 0 }; - cstUtils.jumpToSlice(viewport.element, options); - }, - lastImage: () => { + /** Jumps the active viewport or the specified one to the given slice index */ + jumpToImage: ({ imageIndex, viewport: gridViewport }): void => { // Get current active viewport (return if none active) - const enabledElement = _getActiveViewportEnabledElement(); - if (!enabledElement) { - return; + let viewport; + if (!gridViewport) { + const enabledElement = _getActiveViewportEnabledElement(); + if (!enabledElement) { + return; + } + viewport = enabledElement.viewport; + } else { + viewport = cornerstoneViewportService.getCornerstoneViewport( + gridViewport.id + ); } - const { viewport } = enabledElement; // Get number of slices // -> Copied from cornerstone3D jumpToSlice\_getImageSliceData() @@ -525,8 +518,14 @@ function commandsModule({ servicesManager, commandsManager }) { throw new Error('Unsupported viewport type'); } + const jumpIndex = + imageIndex < 0 ? numberOfSlices + imageIndex : imageIndex; + if (jumpIndex >= numberOfSlices || jumpIndex < 0) { + throw new Error(`Can't jump to ${imageIndex}`); + } + // Set slice to last slice - const options = { imageIndex: numberOfSlices - 1 }; + const options = { imageIndex: jumpIndex }; cstUtils.jumpToSlice(viewport.element, options); }, scroll: ({ direction }) => { @@ -625,8 +624,6 @@ function commandsModule({ servicesManager, commandsManager }) { getNearbyToolData: { commandFn: actions.getNearbyToolData, - storeContexts: [], - options: {}, }, getNearbyAnnotation: { commandFn: actions.getNearbyAnnotation, @@ -636,142 +633,100 @@ function commandsModule({ servicesManager, commandsManager }) { deleteMeasurement: { commandFn: actions.deleteMeasurement, - storeContexts: [], - options: {}, }, setMeasurementLabel: { commandFn: actions.setMeasurementLabel, - storeContexts: [], - options: {}, }, updateMeasurement: { commandFn: actions.updateMeasurement, - storeContexts: [], - options: {}, }, setWindowLevel: { commandFn: actions.setWindowLevel, - storeContexts: [], - options: {}, }, toolbarServiceRecordInteraction: { commandFn: actions.toolbarServiceRecordInteraction, - storeContexts: [], - options: {}, }, setToolActive: { commandFn: actions.setToolActive, - storeContexts: [], - options: {}, }, rotateViewportCW: { commandFn: actions.rotateViewport, - storeContexts: [], options: { rotation: 90 }, }, rotateViewportCCW: { commandFn: actions.rotateViewport, - storeContexts: [], options: { rotation: -90 }, }, incrementActiveViewport: { commandFn: actions.incrementActiveViewport, - storeContexts: [], }, decrementActiveViewport: { commandFn: actions.decrementActiveViewport, - storeContexts: [], }, flipViewportHorizontal: { commandFn: actions.flipViewportHorizontal, - storeContexts: [], - options: {}, }, flipViewportVertical: { commandFn: actions.flipViewportVertical, - storeContexts: [], - options: {}, }, invertViewport: { commandFn: actions.invertViewport, - storeContexts: [], - options: {}, }, resetViewport: { commandFn: actions.resetViewport, - storeContexts: [], - options: {}, }, scaleUpViewport: { commandFn: actions.scaleViewport, - storeContexts: [], options: { direction: 1 }, }, scaleDownViewport: { commandFn: actions.scaleViewport, - storeContexts: [], options: { direction: -1 }, }, fitViewportToWindow: { commandFn: actions.scaleViewport, - storeContexts: [], options: { direction: 0 }, }, nextImage: { commandFn: actions.scroll, - storeContexts: [], options: { direction: 1 }, }, previousImage: { commandFn: actions.scroll, - storeContexts: [], options: { direction: -1 }, }, firstImage: { - commandFn: actions.firstImage, - storeContexts: [], - options: {}, + commandFn: actions.jumpToImage, + options: { imageIndex: 0 }, }, lastImage: { - commandFn: actions.lastImage, - storeContexts: [], - options: {}, + commandFn: actions.jumpToImage, + options: { imageIndex: -1 }, + }, + jumpToImage: { + commandFn: actions.jumpToImage, }, showDownloadViewportModal: { commandFn: actions.showDownloadViewportModal, - storeContexts: [], - options: {}, }, toggleCine: { commandFn: actions.toggleCine, - storeContexts: [], - options: {}, }, arrowTextCallback: { commandFn: actions.arrowTextCallback, - storeContexts: [], - options: {}, }, setViewportActive: { commandFn: actions.setViewportActive, - storeContexts: [], - options: {}, }, setViewportColormap: { commandFn: actions.setViewportColormap, - storeContexts: [], - options: {}, }, toggleStackImageSync: { commandFn: actions.toggleStackImageSync, - storeContexts: [], - options: {}, }, toggleReferenceLines: { commandFn: actions.toggleReferenceLines, - storeContexts: [], - options: {}, }, }; diff --git a/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts b/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts index 447dfd654..31ea90cb2 100644 --- a/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts +++ b/extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts @@ -16,14 +16,14 @@ const VOLUME_LOADER_SCHEME = 'cornerstoneStreamingImageVolume'; class CornerstoneCacheService { static REGISTRATION = { - name: 'cornerstoneCacheService', - altName: 'CornerstoneCacheService', + name: 'cornerstoneCacheService', + altName: 'CornerstoneCacheService', create: ({ servicesManager, }: Types.Extensions.ExtensionParams): CornerstoneCacheService => { return new CornerstoneCacheService(servicesManager); - }, - }; + }, + }; stackImageIds: Map = new Map(); volumeImageIds: Map = new Map(); @@ -143,13 +143,18 @@ class CornerstoneCacheService { this.stackImageIds.set(displaySet.displaySetInstanceUID, stackImageIds); } - const { displaySetInstanceUID, StudyInstanceUID } = displaySet; + const { + displaySetInstanceUID, + StudyInstanceUID, + isCompositeStack, + } = displaySet; const StackViewportData: StackViewportData = { viewportType, data: { StudyInstanceUID, displaySetInstanceUID, + isCompositeStack, imageIds: stackImageIds, }, }; diff --git a/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts b/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts index cf47cce78..012c69e6a 100644 --- a/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts +++ b/extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts @@ -906,6 +906,34 @@ class CornerstoneViewportService extends PubSubService return images[0].FrameOfReferenceUID; } } + + /** + * Looks through the viewports to see if the specified measurement can be + * displayed in one of the viewports. + * + * @param measurement + * The measurement that is desired to view. + * @param activeViewportIndex - the index that was active at the time the jump + * was initiated. + * @return the viewportIndex to display the given measurement + */ + public getViewportIndexToJump( + activeViewportIndex: number, + displaySetInstanceUID: string, + cameraProps: unknown + ): number { + const viewportInfo = this.viewportsInfo.get(activeViewportIndex); + const { referencedImageId } = cameraProps; + if (viewportInfo?.contains(displaySetInstanceUID, referencedImageId)) { + return activeViewportIndex; + } + + return ( + [...this.viewportsById.values()].find(viewportInfo => + viewportInfo.contains(displaySetInstanceUID, referencedImageId) + )?.viewportIndex ?? -1 + ); + } } export default CornerstoneViewportService; diff --git a/extensions/cornerstone/src/services/ViewportService/Viewport.ts b/extensions/cornerstone/src/services/ViewportService/Viewport.ts index c56af0836..a99fa56af 100644 --- a/extensions/cornerstone/src/services/ViewportService/Viewport.ts +++ b/extensions/cornerstone/src/services/ViewportService/Viewport.ts @@ -88,6 +88,20 @@ export type DisplaySet = { const STACK = 'stack'; const DEFAULT_TOOLGROUP_ID = 'default'; +// Return true if the data contains the given display set UID OR the imageId +// if it is a composite object. +const dataContains = ( + data, + displaySetUID: string, + imageId?: string +): boolean => { + if (data.displaySetInstanceUID === displaySetUID) return true; + if (imageId && data.isCompositeStack && data.imageIds) { + return !!data.imageIds.find(dataId => dataId === imageId); + } + return false; +}; + class ViewportInfo { private viewportId = ''; private viewportIndex: number; @@ -104,6 +118,21 @@ class ViewportInfo { this.setPublicDisplaySetOptions([{}]); } + /** + * Return true if the viewport contains the given display set UID, + * OR if it is a composite stack and contains the given imageId + */ + public contains(displaySetUID: string, imageId: string): boolean { + if (!this.viewportData?.data) return false; + + if (this.viewportData.data.length) { + return !!this.viewportData.find(data => + dataContains(data, displaySetUID, imageId) + ); + } + return dataContains(this.viewportData.data, displaySetUID, imageId); + } + public destroy = (): void => { this.element = null; this.viewportData = null; diff --git a/extensions/cornerstone/src/types/CornerstoneCacheService.ts b/extensions/cornerstone/src/types/CornerstoneCacheService.ts index 2a877e9c0..ba79745a0 100644 --- a/extensions/cornerstone/src/types/CornerstoneCacheService.ts +++ b/extensions/cornerstone/src/types/CornerstoneCacheService.ts @@ -1,12 +1,12 @@ -import { - Enums, - Types, -} from '@cornerstonejs/core'; - +import { Enums, Types } from '@cornerstonejs/core'; type StackData = { StudyInstanceUID: string; displaySetInstanceUID: string; + // A composite stack is one created from other display sets - kind of like + // madeInClient, but specific to indicating that the imageIds can come from + // different series or even studies. + isCompositeStack?: boolean; imageIds: string[]; frameRate?: number; isClip?: boolean; @@ -20,19 +20,14 @@ type VolumeData = { imageIds?: string[]; }; - type StackViewportData = { +type StackViewportData = { viewportType: Enums.ViewportType; data: StackData; }; - type VolumeViewportData = { +type VolumeViewportData = { viewportType: Enums.ViewportType; data: VolumeData[]; }; -export type { - StackViewportData, - VolumeViewportData, - StackData, - VolumeData, -}; +export type { StackViewportData, VolumeViewportData, StackData, VolumeData }; diff --git a/extensions/cornerstone/src/utils/measurementServiceMappings/Length.ts b/extensions/cornerstone/src/utils/measurementServiceMappings/Length.ts index 8dad5a1c1..44cf64ac0 100644 --- a/extensions/cornerstone/src/utils/measurementServiceMappings/Length.ts +++ b/extensions/cornerstone/src/utils/measurementServiceMappings/Length.ts @@ -188,6 +188,7 @@ function getDisplayText(mappedAnnotations, displaySet) { const instanceText = InstanceNumber ? ` I: ${InstanceNumber}` : ''; const frameText = displaySet.isMultiFrame ? ` F: ${frameNumber}` : ''; + if (length === null || length === undefined) return displayText; const roundedLength = utils.roundNumber(length, 2); displayText.push( `${roundedLength} mm (S: ${SeriesNumber}${instanceText}${frameText})` diff --git a/extensions/default/src/commandsModule.ts b/extensions/default/src/commandsModule.ts index 172f00921..238cd37ff 100644 --- a/extensions/default/src/commandsModule.ts +++ b/extensions/default/src/commandsModule.ts @@ -1,4 +1,4 @@ -import { ServicesManager, utils } from '@ohif/core'; +import { ServicesManager, utils, Types } from '@ohif/core'; import { ContextMenuController, @@ -244,6 +244,12 @@ const commandsModule = ({ } } // Do this after successfully applying the update + // Note, don't store the active display set - it is only needed while + // changing display sets. This causes jump to measurement to fail on + // multi-study display. + delete displaySetSelectorMap[ + `${activeStudyUID || hpInfo.activeStudyUID}:activeDisplaySet:0` + ]; stateSyncService.store(stateSyncReduce); // This is a default action applied actions.toggleHpTools(hangingProtocolService.getActiveProtocol()); diff --git a/extensions/measurement-tracking/src/contexts/TrackedMeasurementsContext/TrackedMeasurementsContext.tsx b/extensions/measurement-tracking/src/contexts/TrackedMeasurementsContext/TrackedMeasurementsContext.tsx index f73707220..2a5b0a72d 100644 --- a/extensions/measurement-tracking/src/contexts/TrackedMeasurementsContext/TrackedMeasurementsContext.tsx +++ b/extensions/measurement-tracking/src/contexts/TrackedMeasurementsContext/TrackedMeasurementsContext.tsx @@ -47,6 +47,15 @@ function TrackedMeasurementsContextProvider( const uid = trackedMeasurements[0].uid; + console.log( + 'jumping to measurement reset viewport', + viewportGrid.activeViewportIndex, + trackedMeasurements[0] + ); + viewportGridService.setDisplaySetsForViewport({ + viewportIndex: viewportGrid.activeViewportIndex, + displaySetInstanceUIDs: [trackedMeasurements[0].displaySetInstanceUID], + }); measurementService.jumpToMeasurement( viewportGrid.activeViewportIndex, uid diff --git a/platform/core/src/services/MeasurementService/MeasurementService.ts b/platform/core/src/services/MeasurementService/MeasurementService.ts index b1d3e5af7..b3c0b3138 100644 --- a/platform/core/src/services/MeasurementService/MeasurementService.ts +++ b/platform/core/src/services/MeasurementService/MeasurementService.ts @@ -67,7 +67,10 @@ const EVENTS = { RAW_MEASUREMENT_ADDED: 'event::raw_measurement_added', MEASUREMENT_REMOVED: 'event::measurement_removed', MEASUREMENTS_CLEARED: 'event::measurements_cleared', - JUMP_TO_MEASUREMENT: 'event:jump_to_measurement', + // Give the viewport a chance to jump to the measurement + JUMP_TO_MEASUREMENT_VIEWPORT: 'event:jump_to_measurement_viewport', + // Give the layout a chance to jump to the measurement + JUMP_TO_MEASUREMENT_LAYOUT: 'event:jump_to_measurement_layout', }; const VALUE_TYPES = { @@ -104,15 +107,16 @@ class MeasurementService extends PubSubService { }, }; + public static readonly EVENTS = EVENTS; public static VALUE_TYPES = VALUE_TYPES; public readonly VALUE_TYPES = VALUE_TYPES; + private measurements = new Map(); + constructor() { super(EVENTS); this.sources = {}; this.mappings = {}; - this.measurements = {}; - this._jumpToMeasurementCache = {}; } /** @@ -120,7 +124,7 @@ class MeasurementService extends PubSubService { * This method should be used to add custom tool schema to the measurement service. * @param {Array} schema schema for validation */ - addMeasurementSchemaKeys(schema) { + public addMeasurementSchemaKeys(schema): void { if (!Array.isArray(schema)) { schema = [schema]; } @@ -160,11 +164,7 @@ class MeasurementService extends PubSubService { * @return {Measurement[]} Array of measurements */ getMeasurements() { - const measurements = this._arrayOfObjects(this.measurements); - return ( - measurements && - measurements.map(m => this.measurements[Object.keys(m)[0]]) - ); + return [...this.measurements.values()]; } /** @@ -173,18 +173,14 @@ class MeasurementService extends PubSubService { * @param {string} uid measurement uid * @return {Measurement} Measurement instance */ - getMeasurement(measurementUID) { - let measurement = null; - const measurements = this.measurements[measurementUID]; - - if (measurements && Object.keys(measurements).length > 0) { - measurement = this.measurements[measurementUID]; - } - - return measurement; + public getMeasurement(measurementUID: string) { + return this.measurements.get(measurementUID); } - setMeasurementSelected(measurementUID, selected) { + public setMeasurementSelected( + measurementUID: string, + selected: boolean + ): void { const measurement = this.getMeasurement(measurementUID); if (!measurement) { return; @@ -373,8 +369,8 @@ class MeasurementService extends PubSubService { } } - update(measurementUID, measurement, notYetUpdatedAtSource = false) { - if (!this.measurements[measurementUID]) { + update(measurementUID: string, measurement, notYetUpdatedAtSource = false) { + if (!this.measurements.has(measurementUID)) { return; } @@ -388,7 +384,7 @@ class MeasurementService extends PubSubService { updatedMeasurement ); - this.measurements[measurementUID] = updatedMeasurement; + this.measurements.set(measurementUID, updatedMeasurement); this._broadcastEvent(this.EVENTS.MEASUREMENT_UPDATED, { source: measurement.source, @@ -470,15 +466,15 @@ class MeasurementService extends PubSubService { uid: internalUID, }; - if (this.measurements[internalUID]) { - this.measurements[internalUID] = newMeasurement; + if (this.measurements.get(internalUID)) { + this.measurements.set(internalUID, newMeasurement); this._broadcastEvent(this.EVENTS.MEASUREMENT_UPDATED, { source, measurement: newMeasurement, }); } else { log.info('Measurement added', newMeasurement); - this.measurements[internalUID] = newMeasurement; + this.measurements.set(internalUID, newMeasurement); this._broadcastEvent(this.EVENTS.RAW_MEASUREMENT_ADDED, { source, measurement: newMeasurement, @@ -557,7 +553,7 @@ class MeasurementService extends PubSubService { ); } - const oldMeasurement = this.measurements[internalUID]; + const oldMeasurement = this.measurements.get(internalUID); const newMeasurement = { ...oldMeasurement, @@ -569,7 +565,7 @@ class MeasurementService extends PubSubService { if (oldMeasurement) { // TODO: Ultimately, each annotation should have a selected flag right from the soure. // For now, it is just added in OHIF here and in setMeasurementSelected. - this.measurements[internalUID] = newMeasurement; + this.measurements.set(internalUID, newMeasurement); if (isUpdate) { this._broadcastEvent(this.EVENTS.MEASUREMENT_UPDATED, { source, @@ -585,7 +581,7 @@ class MeasurementService extends PubSubService { } } else { log.info('Measurement started.', newMeasurement); - this.measurements[internalUID] = newMeasurement; + this.measurements.set(internalUID, newMeasurement); } return newMeasurement.uid; @@ -598,12 +594,12 @@ class MeasurementService extends PubSubService { * @param {MeasurementSource} source The measurement source instance */ remove(measurementUID, source, eventDetails) { - if (!measurementUID || !this.measurements[measurementUID]) { + if (!measurementUID || !this.measurements.has(measurementUID)) { log.warn(`No uid provided, or unable to find measurement by uid.`); return; } - delete this.measurements[measurementUID]; + this.measurements.delete(measurementUID); this._broadcastEvent(this.EVENTS.MEASUREMENT_REMOVED, { source, measurement: measurementUID, @@ -613,9 +609,8 @@ class MeasurementService extends PubSubService { clearMeasurements() { // Make a copy of the measurements - const measurements = { ...this.measurements }; - this.measurements = {}; - this._jumpToMeasurementCache = {}; + const measurements = [...this.measurements.values()]; + this.measurements.clear(); this._broadcastEvent(this.EVENTS.MEASUREMENTS_CLEARED, { measurements }); } @@ -628,27 +623,39 @@ class MeasurementService extends PubSubService { this.clearMeasurements(); } - jumpToMeasurement(viewportIndex, measurementUID) { - const measurement = this.measurements[measurementUID]; + /** + * This method calls the subscriptions for JUMP_TO_MEASUREMENT_VIEWPORT + * and JUMP_TO_MEASUREMENT_LAYOUT. There are two events which are + * fired because there are two different items which might want to handle + * the event. First, there might already be a viewport which can handle + * the event. If so, then the layout doesn't need to necessarily change. + * This is communicated by the isConsumed value on the event itself. + * Otherwise, the layout itself may need to be navigated to in order + * to provide a viewport which can show the given measurement. + * + * When a viewport decides to apply the event, it should call the consume() + * method on the event, so that other listeners know they do not need to + * navigate. This does NOT affect whether the layout event is fired, and + * merely causes it to fire the event with the isConsumed set to true. + */ + + public jumpToMeasurement( + viewportIndex: number, + measurementUID: string + ): void { + const measurement = this.measurements.get(measurementUID); if (!measurement) { log.warn(`No measurement uid, or unable to find by uid.`); return; } - this._addJumpToMeasurement(viewportIndex, measurementUID); - - this._broadcastEvent(this.EVENTS.JUMP_TO_MEASUREMENT, { + const consumableEvent = this.createConsumableEvent({ viewportIndex, measurement, }); - } - getJumpToMeasurement(viewportIndex) { - return this._jumpToMeasurementCache[viewportIndex]; - } - - removeJumpToMeasurement(viewportIndex) { - delete this._jumpToMeasurementCache[viewportIndex]; + this._broadcastEvent(EVENTS.JUMP_TO_MEASUREMENT_VIEWPORT, consumableEvent); + this._broadcastEvent(EVENTS.JUMP_TO_MEASUREMENT_LAYOUT, consumableEvent); } _getSourceUID(name, version) { @@ -663,10 +670,6 @@ class MeasurementService extends PubSubService { return sourceUID; } - _addJumpToMeasurement(viewportIndex, measurementUID) { - this._jumpToMeasurementCache[viewportIndex] = measurementUID; - } - _getMappingByMeasurementSource(measurement, annotationType) { if (this._isValidSource(measurement.source)) { return this.mappings[measurement.source.uid].find( diff --git a/platform/core/src/services/ViewportGridService/ViewportGridService.ts b/platform/core/src/services/ViewportGridService/ViewportGridService.ts index 239db4f88..a5fca6e6a 100644 --- a/platform/core/src/services/ViewportGridService/ViewportGridService.ts +++ b/platform/core/src/services/ViewportGridService/ViewportGridService.ts @@ -1,12 +1,13 @@ import { PubSubService } from '../_shared/pubSubServiceInterface'; - -const EVENTS = { - ACTIVE_VIEWPORT_INDEX_CHANGED: 'event::activeviewportindexchanged', - LAYOUT_CHANGED: 'event::layoutChanged', - GRID_STATE_CHANGED: 'event::gridStateChanged', -}; +import { getPresentationIds, PresentationIds } from './getPresentationIds'; class ViewportGridService extends PubSubService { + public static readonly EVENTS = { + ACTIVE_VIEWPORT_INDEX_CHANGED: 'event::activeviewportindexchanged', + LAYOUT_CHANGED: 'event::layoutChanged', + GRID_STATE_CHANGED: 'event::gridStateChanged', + }; + public static REGISTRATION = { name: 'viewportGridService', altName: 'ViewportGridService', @@ -14,12 +15,13 @@ class ViewportGridService extends PubSubService { return new ViewportGridService(); }, }; - public static EVENTS = EVENTS; + + public static getPresentationIds = getPresentationIds; serviceImplementation = {}; constructor() { - super(EVENTS); + super(ViewportGridService.EVENTS); this.serviceImplementation = {}; } @@ -37,10 +39,12 @@ class ViewportGridService extends PubSubService { this.serviceImplementation._getState = getStateImplementation; } if (setActiveViewportIndexImplementation) { - this.serviceImplementation._setActiveViewportIndex = setActiveViewportIndexImplementation; + this.serviceImplementation._setActiveViewportIndex = + setActiveViewportIndexImplementation; } if (setDisplaySetsForViewportsImplementation) { - this.serviceImplementation._setDisplaySetsForViewports = setDisplaySetsForViewportsImplementation; + this.serviceImplementation._setDisplaySetsForViewports = + setDisplaySetsForViewportsImplementation; } if (setLayoutImplementation) { this.serviceImplementation._setLayout = setLayoutImplementation; @@ -55,7 +59,8 @@ class ViewportGridService extends PubSubService { this.serviceImplementation._set = setImplementation; } if (getNumViewportPanesImplementation) { - this.serviceImplementation._getNumViewportPanes = getNumViewportPanesImplementation; + this.serviceImplementation._getNumViewportPanes = + getNumViewportPanesImplementation; } } @@ -75,11 +80,29 @@ class ViewportGridService extends PubSubService { public setDisplaySetsForViewport(props) { // Just update a single viewport, but use the multi-viewport update for it. - this.serviceImplementation._setDisplaySetsForViewports([props]); + this.setDisplaySetsForViewports([props]); } public setDisplaySetsForViewports(props) { this.serviceImplementation._setDisplaySetsForViewports(props); + const state = this.getState(); + const viewports = []; + + for (const viewport of props) { + const updatedViewport = state.viewports[viewport.viewportIndex]; + if (updatedViewport) { + viewports.push(updatedViewport); + } else { + console.warn( + "ViewportGridService::Didn't find updated viewport", + viewport + ); + } + } + this._broadcastEvent(ViewportGridService.EVENTS.GRID_STATE_CHANGED, { + state, + viewports, + }); } /** @@ -150,3 +173,5 @@ class ViewportGridService extends PubSubService { } export default ViewportGridService; + +export type { PresentationIds }; diff --git a/platform/ui/src/contextProviders/getPresentationIds.ts b/platform/core/src/services/ViewportGridService/getPresentationIds.ts similarity index 99% rename from platform/ui/src/contextProviders/getPresentationIds.ts rename to platform/core/src/services/ViewportGridService/getPresentationIds.ts index b34b6badc..429917511 100644 --- a/platform/ui/src/contextProviders/getPresentationIds.ts +++ b/platform/core/src/services/ViewportGridService/getPresentationIds.ts @@ -118,3 +118,4 @@ const getPresentationIds = (viewport, viewports): PresentationIds => { }; export default getPresentationIds; +export { getPresentationIds }; diff --git a/platform/core/src/services/_shared/pubSubServiceInterface.js b/platform/core/src/services/_shared/pubSubServiceInterface.js index 20b5f27d7..7d4460fda 100644 --- a/platform/core/src/services/_shared/pubSubServiceInterface.js +++ b/platform/core/src/services/_shared/pubSubServiceInterface.js @@ -103,4 +103,20 @@ export class PubSubService { this.unsubscriptions.forEach(unsub => unsub()); this.unsubscriptions = []; } + + /** + * Creates an event that records whether or not someone + * has consumed it. Call eventData.consume() to consume the event. + * Check eventData.isConsumed to see if it is consumed or not. + * @param props - to include in the event + */ + protected createConsumableEvent(props) { + return { + ...props, + isConsumed: false, + consume: function Consume() { + this.isConsumed = true; + }, + } + } } diff --git a/platform/core/src/utils/absoluteUrl.test.js b/platform/core/src/utils/absoluteUrl.test.js index 7e69f69b2..fe923064d 100644 --- a/platform/core/src/utils/absoluteUrl.test.js +++ b/platform/core/src/utils/absoluteUrl.test.js @@ -24,27 +24,22 @@ describe('absoluteUrl', () => { }); test('should return the original path when there path in the window.origin after the domain and port', () => { - global.window = Object.create(window); + delete global.window.location; const url = 'http://dummy.com'; - Object.defineProperty(window, 'location', { - value: { - origin: url, - }, - writable: true, - }); + global.window.location = { + origin: url, + }; const absoluteUrlOutput = absoluteUrl('path_1/path_2/path_3'); expect(absoluteUrlOutput).toEqual('/path_1/path_2/path_3'); }); test('should be able to return the absolute path even when the path contains duplicates', () => { - global.window = Object.create(window); + global.window ||= Object.create(window); const url = 'http://dummy.com'; - Object.defineProperty(window, 'location', { - value: { - origin: url, - }, - writable: true, - }); + delete global.window.location; + global.window.location = { + origin: url, + }; const absoluteUrlOutput = absoluteUrl('path_1/path_1/path_1'); expect(absoluteUrlOutput).toEqual('/path_1/path_1/path_1'); }); diff --git a/platform/docs/docs/platform/services/data/MeasurementService.md b/platform/docs/docs/platform/services/data/MeasurementService.md index 74605bce1..21bd4589f 100644 --- a/platform/docs/docs/platform/services/data/MeasurementService.md +++ b/platform/docs/docs/platform/services/data/MeasurementService.md @@ -29,7 +29,8 @@ There are seven events that get publish in `MeasurementService`: | RAW_MEASUREMENT_ADDED | Fires when a raw measurement is added (e.g., dicom-sr) | | MEASUREMENT_REMOVED | Fires when a measurement is removed | | MEASUREMENTS_CLEARED | Fires when all measurements are deleted | -| JUMP_TO_MEASUREMENT | Fires when a measurement is requested to be jump to | +| JUMP_TO_MEASUREMENT_VIEWPORT | Fires when a measurement is requested to be jumped to, applying to individual viewports. | +| JUMP_TO_MEASUREMENT_LAYOUT | Fires when a measurement is requested to be jumped to, applying to the overall layout. | ## API diff --git a/platform/ui/src/contextProviders/ViewportGridProvider.tsx b/platform/ui/src/contextProviders/ViewportGridProvider.tsx index 85fbb45db..1ac89e519 100644 --- a/platform/ui/src/contextProviders/ViewportGridProvider.tsx +++ b/platform/ui/src/contextProviders/ViewportGridProvider.tsx @@ -7,8 +7,8 @@ import React, { } from 'react'; import PropTypes from 'prop-types'; import isEqual from 'lodash.isequal'; +import { ViewportGridService } from '@ohif/core'; import viewportLabels from '../utils/viewportLabels'; -import getPresentationIds from './getPresentationIds'; const DEFAULT_STATE = { activeViewportIndex: 0, @@ -173,7 +173,7 @@ export function ViewportGridProvider({ children, service }) { displaySetOptions, viewportLabel: viewportLabels[viewportIndex], }; - viewportOptions.presentationIds = getPresentationIds( + viewportOptions.presentationIds = ViewportGridService.getPresentationIds( newViewport, viewports ); @@ -265,7 +265,7 @@ export function ViewportGridProvider({ children, service }) { state.viewports ); if (!viewport.viewportOptions.presentationIds) { - viewport.viewportOptions.presentationIds = getPresentationIds( + viewport.viewportOptions.presentationIds = ViewportGridService.getPresentationIds( viewport, viewports ); @@ -403,12 +403,16 @@ export function ViewportGridProvider({ children, service }) { getNumViewportPanes, ]); + // run many of the calls through the service itself since we want to publish events const api = { getState, - setActiveViewportIndex: index => service.setActiveViewportIndex(index), // run it through the service itself since we want to publish events - setDisplaySetsForViewports, - setLayout: layout => service.setLayout(layout), // run it through the service itself since we want to publish events - reset, + setActiveViewportIndex: index => service.setActiveViewportIndex(index), + setDisplaySetsForViewport: props => + service.setDisplaySetsForViewports([props]), + setDisplaySetsForViewports: props => + service.setDisplaySetsForViewports(props), + setLayout: layout => service.setLayout(layout), + reset: () => service.reset(), set: gridLayoutState => service.setState(gridLayoutState), // run it through the service itself since we want to publish events getNumViewportPanes, }; @@ -422,9 +426,7 @@ export function ViewportGridProvider({ children, service }) { ViewportGridProvider.propTypes = { children: PropTypes.any, - service: PropTypes.shape({ - setServiceImplementation: PropTypes.func, - }).isRequired, + service: PropTypes.instanceOf(ViewportGridService).isRequired, }; export const useViewportGrid = () => useContext(ViewportGridContext); diff --git a/platform/ui/src/types/index.ts b/platform/ui/src/types/index.ts index 5d0729fbe..284eea278 100644 --- a/platform/ui/src/types/index.ts +++ b/platform/ui/src/types/index.ts @@ -18,4 +18,4 @@ const StringNumber = PropTypes.oneOfType([PropTypes.string, PropTypes.number]); */ const StringArray = PropTypes.oneOfType([PropTypes.string, PropTypes.array]); -export { StringNumber, StringArray, ThumbnailType, PresentationIds }; +export { StringNumber, StringArray, ThumbnailType }; diff --git a/platform/viewer/src/components/ViewportGrid.tsx b/platform/viewer/src/components/ViewportGrid.tsx index ca2cc71cc..dea53511c 100644 --- a/platform/viewer/src/components/ViewportGrid.tsx +++ b/platform/viewer/src/components/ViewportGrid.tsx @@ -1,6 +1,6 @@ import React, { useEffect, useCallback } from 'react'; import PropTypes from 'prop-types'; -import { ServicesManager, Types } from '@ohif/core'; +import { ServicesManager, Types, MeasurementService } from '@ohif/core'; import { ViewportGrid, ViewportPane, useViewportGrid } from '@ohif/ui'; import { utils } from '@ohif/core'; import EmptyViewport from './EmptyViewport'; @@ -23,13 +23,6 @@ const ORIENTATION_MAP = { }, }; -const compareViewportOptions = (opts1, opts2) => { - if ((opts1.viewportType || 'stack') != opts2.viewportType) { - return false; - } - return true; -}; - function ViewerViewportGrid(props) { const { servicesManager, viewportComponents, dataSource } = props; const [viewportGrid, viewportGridService] = useViewportGrid(); @@ -160,77 +153,48 @@ function ViewerViewportGrid(props) { useEffect(() => { const { unsubscribe } = measurementService.subscribe( - measurementService.EVENTS.JUMP_TO_MEASUREMENT, - ({ viewportIndex, measurement }) => { - const { - displaySetInstanceUID: referencedDisplaySetInstanceUID, - metadata: { viewPlaneNormal }, - } = measurement; - - // if we already have the displaySet in one of the viewports - // Todo: handle fusion display sets? - for (const viewport of viewports) { - const isMatch = viewport.displaySetInstanceUIDs.includes( - referencedDisplaySetInstanceUID - ); - if (isMatch) { - return; - } - } - - const displaySet = displaySetService.getDisplaySetByUID( - referencedDisplaySetInstanceUID - ); - - let imageIndex; - // jump straight to the initial image index if we can - if (displaySet.images && measurement.SOPInstanceUID) { - imageIndex = displaySet.images.findIndex( - image => image.SOPInstanceUID === measurement.SOPInstanceUID - ); - } + MeasurementService.EVENTS.JUMP_TO_MEASUREMENT_LAYOUT, + ({ viewportIndex, measurement, isConsumed }) => { + if (isConsumed) return; + // This occurs when no viewport has elected to consume the event + // so we need to change layouts into a layout which can consume + // the event. + const { displaySetInstanceUID: referencedDisplaySetInstanceUID } = + measurement; const updatedViewports = _getUpdatedViewports( viewportIndex, referencedDisplaySetInstanceUID ); + // Arbitrarily assign the viewport to element 0 + const viewport = updatedViewports?.[0]; - if (!updatedViewports || !updatedViewports.length) { + if (!viewport) { + console.warn( + 'ViewportGrid::Unable to navigate to viewport containing', + referencedDisplaySetInstanceUID + ); return; } - updatedViewports.forEach(vp => { - vp.viewportOptions ||= {}; - const { orientation, viewportType } = vp.viewportOptions; - let initialImageOptions; + viewport.viewportOptions ||= {}; + viewport.viewportOptions.orientation = 'acquisition'; - // For initial imageIndex to hang be careful for the volume viewport - if (viewportType === 'stack' || !viewportType) { - initialImageOptions = { - index: imageIndex, - }; - } else if (viewportType === 'volume') { - // For the volume viewports, be careful to not jump in the viewports - // that are not in the same orientation. - // Todo: this doesn't work for viewports that have custom orientation - // vectors specified - if ( - orientation && - viewPlaneNormal && - isEqualWithin( - ORIENTATION_MAP[orientation]?.viewPlaneNormal, - viewPlaneNormal - ) - ) { - initialImageOptions = { - index: imageIndex, + const displaySet = displaySetService.getDisplaySetByUID( + referencedDisplaySetInstanceUID + ); + // jump straight to the initial image index if we can + if (displaySet.images && measurement.SOPInstanceUID) { + for (let index = 0; index < displaySet.images.length; index++) { + const image = displaySet.images[index]; + if (image.SOPInstanceUID === measurement.SOPInstanceUID) { + viewport.viewportOptions.initialImageOptions = { + index, }; + break; } } - - vp.viewportOptions.initialImageOptions = initialImageOptions; - }); - + } viewportGridService.setDisplaySetsForViewports(updatedViewports); } ); diff --git a/yarn.lock b/yarn.lock index d8eda8ae3..6b51fc00e 100644 --- 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"https://registry.npmjs.org/source-list-map/-/source-list-map-2.0.1.tgz#3993bd873bfc48479cca9ea3a547835c7c154b34" @@ -20823,6 +21091,11 @@ timsort@^0.3.0: resolved "https://registry.npmjs.org/timsort/-/timsort-0.3.0.tgz#405411a8e7e6339fe64db9a234de11dc31e02bd4" integrity sha512-qsdtZH+vMoCARQtyod4imc2nIJwg9Cc7lPRrw9CzF8ZKR0khdr8+2nX80PBhET3tcyTtJDxAffGh2rXH4tyU8A== +tiny-emitter@^2.1.0: + version "2.1.0" + resolved "https://registry.yarnpkg.com/tiny-emitter/-/tiny-emitter-2.1.0.tgz#1d1a56edfc51c43e863cbb5382a72330e3555423" + integrity sha512-NB6Dk1A9xgQPMoGqC5CVXn123gWyte215ONT5Pp5a0yt4nlEoO1ZWeCwpncaekPHXO60i47ihFnZPiRPjRMq4Q== + tiny-invariant@^1.0.2: version "1.3.1" resolved "https://registry.npmjs.org/tiny-invariant/-/tiny-invariant-1.3.1.tgz#8560808c916ef02ecfd55e66090df23a4b7aa642" @@ -21084,6 +21357,11 @@ typed-array-length@^1.0.4: for-each "^0.3.3" is-typed-array "^1.1.9" +typed-function@^4.1.0: + version "4.1.0" + resolved "https://registry.yarnpkg.com/typed-function/-/typed-function-4.1.0.tgz#da4bdd8a6d19a89e22732f75e4a410860aaf9712" + integrity sha512-DGwUl6cioBW5gw2L+6SMupGwH/kZOqivy17E4nsh1JI9fKF87orMmlQx3KISQPmg3sfnOUGlwVkroosvgddrlg== + typedarray-to-buffer@^3.1.5: version "3.1.5" resolved "https://registry.npmjs.org/typedarray-to-buffer/-/typedarray-to-buffer-3.1.5.tgz#a97ee7a9ff42691b9f783ff1bc5112fe3fca9080" @@ -21580,7 +21858,7 @@ uuid@^8.3.2: resolved "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz#80d5b5ced271bb9af6c445f21a1a04c606cefbe2" integrity sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg== -uuid@^9.0.0: +uuid@^9.0, uuid@^9.0.0: version "9.0.0" resolved "https://registry.npmjs.org/uuid/-/uuid-9.0.0.tgz#592f550650024a38ceb0c562f2f6aa435761efb5" integrity sha512-MXcSTerfPa4uqyzStbRoTgt5XIe3x5+42+q1sDuy3R5MDk66URdLMOZe5aPX/SQd+kuYAh0FdP/pO28IkQyTeg== @@ -21779,6 +22057,11 @@ web-streams-polyfill@^3.0.3: resolved 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"https://registry.yarnpkg.com/xml-utils/-/xml-utils-1.7.0.tgz#333ce391d8918f872aaf98d2cf90f9ef9b82bd0f" + integrity sha512-bWB489+RQQclC7A9OW8e5BzbT8Tu//jtAOvkYwewFr+Q9T9KDGvfzC1lp0pYPEQPEoPQLDkmxkepSC/2gIAZGw== + xml@^1.0.1: version "1.0.1" resolved "https://registry.npmjs.org/xml/-/xml-1.0.1.tgz#78ba72020029c5bc87b8a81a3cfcd74b4a2fc1e5" From 0e3491d6bb460682f47ade53f8077b6dc85e2a9a Mon Sep 17 00:00:00 2001 From: David Smith Date: Mon, 1 May 2023 12:58:53 -0400 Subject: [PATCH 24/54] feat(proxy datasource): JSON server configuration launch (#2791) * feat: delegating dicom web proxy datasource * fix: configurably allow WADO image loader to issue preflight OPTIONS request * Added documentation and fixed up some error handling from PR review * review comments changes * another small code review fix --- .../src/DicomWebProxyDataSource/index.js | 84 +++++++++++++++++++ .../default/src/getDataSourcesModule.js | 6 ++ .../dataSources/dicom-web-proxy.md | 54 ++++++++++++ platform/viewer/public/config/default.js | 8 ++ 4 files changed, 152 insertions(+) create mode 100644 extensions/default/src/DicomWebProxyDataSource/index.js create mode 100644 platform/docs/docs/configuration/dataSources/dicom-web-proxy.md diff --git a/extensions/default/src/DicomWebProxyDataSource/index.js b/extensions/default/src/DicomWebProxyDataSource/index.js new file mode 100644 index 000000000..e873237dd --- /dev/null +++ b/extensions/default/src/DicomWebProxyDataSource/index.js @@ -0,0 +1,84 @@ +import { IWebApiDataSource } from '@ohif/core'; +import { createDicomWebApi } from '../DicomWebDataSource/index'; + +/** + * This datasource is initialized with a url that returns a JSON object with a + * dicomWeb datasource configuration array present in a "servers" object. + * + * Only the first array item is parsed, if there are multiple items in the + * dicomWeb configuration array + * + */ +function createDicomWebProxyApi( + dicomWebProxyConfig, + UserAuthenticationService +) { + const { name } = dicomWebProxyConfig; + let dicomWebDelegate = undefined; + + const implementation = { + initialize: async ({ params, query }) => { + let studyInstanceUIDs = []; + + // there seem to be a couple of variations of the case for this parameter + const queryStudyInstanceUIDs = + query.get('studyInstanceUIDs') || query.get('studyInstanceUids'); + if (!queryStudyInstanceUIDs) { + throw new Error(`No studyInstanceUids in request for '${name}'`); + } + + const url = query.get('url'); + + if (!url) { + throw new Error(`No url for '${name}'`); + } else { + const response = await fetch(url); + let data = await response.json(); + if (!data.servers?.dicomWeb?.[0]) { + throw new Error('Invalid configuration returned by url'); + } + + dicomWebDelegate = createDicomWebApi( + data.servers.dicomWeb[0], + UserAuthenticationService + ); + studyInstanceUIDs = queryStudyInstanceUIDs.split(';'); + } + return studyInstanceUIDs; + }, + query: { + studies: { + search: params => dicomWebDelegate.query.studies.search(params), + }, + series: { + search: (...args) => dicomWebDelegate.query.series.search(...args), + }, + instances: { + search: (studyInstanceUid, queryParameters) => + dicomWebDelegate.query.instances.search( + studyInstanceUid, + queryParameters + ), + }, + }, + retrieve: { + directURL: (...args) => dicomWebDelegate.retrieve.directURL(...args), + series: { + metadata: (...args) => + dicomWebDelegate.retrieve.series.metadata(...args), + }, + }, + store: { + dicom: (...args) => dicomWebDelegate.store(...args), + }, + deleteStudyMetadataPromise: (...args) => + dicomWebDelegate.deleteStudyMetadataPromise(...args), + getImageIdsForDisplaySet: (...args) => + dicomWebDelegate.getImageIdsForDisplaySet(...args), + getImageIdsForInstance: (...args) => + dicomWebDelegate.getImageIdsForInstance(...args), + }; + return IWebApiDataSource.create(implementation); +} + +export { createDicomWebProxyApi }; diff --git a/extensions/default/src/getDataSourcesModule.js b/extensions/default/src/getDataSourcesModule.js index dfccc6a18..6eab56a2f 100644 --- a/extensions/default/src/getDataSourcesModule.js +++ b/extensions/default/src/getDataSourcesModule.js @@ -5,6 +5,7 @@ import { createDicomWebApi } from './DicomWebDataSource/index.js'; import { createDicomJSONApi } from './DicomJSONDataSource/index.js'; import { createDicomLocalApi } from './DicomLocalDataSource/index.js'; +import { createDicomWebProxyApi } from './DicomWebProxyDataSource/index.js'; /** * @@ -16,6 +17,11 @@ function getDataSourcesModule() { type: 'webApi', createDataSource: createDicomWebApi, }, + { + name: 'dicomwebproxy', + type: 'webApi', + createDataSource: createDicomWebProxyApi, + }, { name: 'dicomjson', type: 'jsonApi', diff --git a/platform/docs/docs/configuration/dataSources/dicom-web-proxy.md b/platform/docs/docs/configuration/dataSources/dicom-web-proxy.md new file mode 100644 index 000000000..6f98b36a4 --- /dev/null +++ b/platform/docs/docs/configuration/dataSources/dicom-web-proxy.md @@ -0,0 +1,54 @@ +--- +sidebar_position: 4 +sidebar_label: DICOMweb Proxy +--- + +# DICOMweb Proxy + +You can launch the OHIF Viewer with a url that returns a JSON file which +contains a DICOMWeb configuration. The DICOMweb Proxy constructs a DICOMweb +datasource and delegates subsequent requests for metadata and images to that. + +Usage is similar to that of the [DICOM JSON](./dicom-json.md) datasource and +might look like + +`https://v3-demo.ohif.org/viewer/dicomwebproxy?url=https://ohif-dicom-json-example.s3.amazonaws.com/dicomweb.json` + +The url to the location of the JSON file is passed in the query +after the `dicomwebproxy` string, which is +`https://ohif-dicom-json-example.s3.amazonaws.com/dicomweb.json` (this json file +does not exist at the moment of this writing). + +## DICOMweb JSON configuration sample + +The json returned by the url in this example contains a dicomweb configuration +(see [DICOMweb](dicom-web.md)), in a "servers" object, which is then used to +construct a dynamic DICOMweb datasource to delegate requests to. Here is an +example configuration that might be returned using the url parameter. + +```json +{ + "servers": { + "dicomWeb": [ + { + "name": "DCM4CHEE", + "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", + "qidoSupportsIncludeField": true, + "supportsReject": true, + "imageRendering": "wadors", + "thumbnailRendering": "wadors", + "enableStudyLazyLoad": true, + "supportsFuzzyMatching": true, + "supportsWildcard": true + } + ] + } +} +``` + +The DICOMweb Proxy expects the json returned by the url parameter it is invoked +with to include a servers object which contains a "dicomWeb" configuration array +as above. It will only consider the first array item in the dicomWeb +configuration. diff --git a/platform/viewer/public/config/default.js b/platform/viewer/public/config/default.js index 558f473c2..05a408969 100644 --- a/platform/viewer/public/config/default.js +++ b/platform/viewer/public/config/default.js @@ -53,6 +53,14 @@ window.config = { useBulkDataURI: false, }, }, + { + friendlyName: 'dicomweb delegating proxy', + namespace: '@ohif/extension-default.dataSourcesModule.dicomwebproxy', + sourceName: 'dicomwebproxy', + configuration: { + name: 'dicomwebproxy', + }, + }, { friendlyName: 'dicom json', namespace: '@ohif/extension-default.dataSourcesModule.dicomjson', From 89936a5b505a568641df9c7918bb0d5d66b9523f Mon Sep 17 00:00:00 2001 From: Pavan Kumar Jadda <17564080+pavankjadda@users.noreply.github.com> Date: Mon, 1 May 2023 20:32:07 -0400 Subject: [PATCH 25/54] chore(lerna): upgrades lerna to 6.x (#3215) * feat(core): upgrades lerna to 6.x.x * feat(core): upgrades lerna to 6.5.1 * feat(core): updates lerna to 6.x.x * feat(core): updates default config --- package.json | 2 +- yarn.lock | 4436 +++++++++++++++++++++++++------------------------- 2 files changed, 2247 insertions(+), 2191 deletions(-) diff --git a/package.json b/package.json index c5287de03..e7dac0b11 100644 --- a/package.json +++ b/package.json @@ -109,7 +109,7 @@ "jest": "^24.8.0", "jest-canvas-mock": "^2.1.0", "jest-junit": "^6.4.0", - "lerna": "^3.15.0", + "lerna": "^6.5.1", "lint-staged": "^9.0.2", "mini-css-extract-plugin": "^2.1.0", "optimize-css-assets-webpack-plugin": "^5.0.3", diff --git a/yarn.lock b/yarn.lock index 6b51fc00e..ab4a1c144 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2337,85 +2337,16 @@ minimatch "^3.0.4" strip-json-comments "^3.1.1" -"@evocateur/libnpmaccess@^3.1.2": - version "3.1.2" - resolved "https://registry.npmjs.org/@evocateur/libnpmaccess/-/libnpmaccess-3.1.2.tgz#ecf7f6ce6b004e9f942b098d92200be4a4b1c845" - integrity 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sha512-WOkpgNhPTlE73h4VFAFsOnomJVaovO8VqLDzy5saChRBFQFBoMYirowyW+Q9HB4HFF4Z7VZTiG3iSzJJA29yRA== + +yargs-parser@21.1.1, yargs-parser@^21.1.1: + version "21.1.1" + resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" + integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== + yargs-parser@^13.1.2: version "13.1.2" resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.2.tgz#130f09702ebaeef2650d54ce6e3e5706f7a4fb38" @@ -22851,19 +22919,24 @@ yargs-parser@^13.1.2: camelcase "^5.0.0" decamelize "^1.2.0" -yargs-parser@^15.0.1: - version "15.0.3" - resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-15.0.3.tgz#316e263d5febe8b38eef61ac092b33dfcc9b1115" - integrity sha512-/MVEVjTXy/cGAjdtQf8dW3V9b97bPN7rNn8ETj6BmAQL7ibC7O1Q9SPJbGjgh3SlwoBNXMzj/ZGIj8mBgl12YA== - dependencies: - camelcase "^5.0.0" - decamelize "^1.2.0" - yargs-parser@^20.2.2, yargs-parser@^20.2.3, yargs-parser@^20.2.9: version "20.2.9" resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz#2eb7dc3b0289718fc295f362753845c41a0c94ee" integrity sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w== +yargs@16.2.0, yargs@^16.2.0: + version "16.2.0" + resolved "https://registry.yarnpkg.com/yargs/-/yargs-16.2.0.tgz#1c82bf0f6b6a66eafce7ef30e376f49a12477f66" + integrity sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw== + dependencies: + cliui "^7.0.2" + escalade "^3.1.1" + get-caller-file "^2.0.5" + require-directory "^2.1.1" + string-width "^4.2.0" + y18n "^5.0.5" + yargs-parser "^20.2.2" + yargs@^13.3.0: version "13.3.2" resolved "https://registry.npmjs.org/yargs/-/yargs-13.3.2.tgz#ad7ffefec1aa59565ac915f82dccb38a9c31a2dd" @@ -22880,35 +22953,18 @@ yargs@^13.3.0: y18n "^4.0.0" yargs-parser "^13.1.2" -yargs@^14.2.2: - version "14.2.3" - resolved "https://registry.npmjs.org/yargs/-/yargs-14.2.3.tgz#1a1c3edced1afb2a2fea33604bc6d1d8d688a414" - integrity sha512-ZbotRWhF+lkjijC/VhmOT9wSgyBQ7+zr13+YLkhfsSiTriYsMzkTUFP18pFhWwBeMa5gUc1MzbhrO6/VB7c9Xg== +yargs@^17.6.2: + version "17.7.2" + resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.2.tgz#991df39aca675a192b816e1e0363f9d75d2aa269" + integrity sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w== dependencies: - cliui "^5.0.0" - decamelize "^1.2.0" - find-up "^3.0.0" - get-caller-file "^2.0.1" - require-directory "^2.1.1" - require-main-filename "^2.0.0" - set-blocking "^2.0.0" - string-width "^3.0.0" - which-module "^2.0.0" - y18n "^4.0.0" - yargs-parser "^15.0.1" - -yargs@^16.2.0: - version "16.2.0" - resolved "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz#1c82bf0f6b6a66eafce7ef30e376f49a12477f66" - integrity sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw== - dependencies: - cliui "^7.0.2" + cliui "^8.0.1" escalade "^3.1.1" get-caller-file "^2.0.5" require-directory "^2.1.1" - string-width "^4.2.0" + string-width "^4.2.3" y18n "^5.0.5" - yargs-parser "^20.2.2" + yargs-parser "^21.1.1" yarn-programmatic@^0.1.2: version "0.1.2" From 0f85b1a681828ce002398ff8d29927ebace316f7 Mon Sep 17 00:00:00 2001 From: Joe Boccanfuso <109477394+jbocce@users.noreply.github.com> Date: Tue, 2 May 2023 09:24:53 -0400 Subject: [PATCH 26/54] fix(DICOM Upload): Decreased the minimum height for the upload dialog contents to better fit some laptops. (#3347) --- .../cornerstone/src/components/DicomUpload/DicomUpload.tsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/extensions/cornerstone/src/components/DicomUpload/DicomUpload.tsx b/extensions/cornerstone/src/components/DicomUpload/DicomUpload.tsx index fa29e65d1..26e596e95 100644 --- a/extensions/cornerstone/src/components/DicomUpload/DicomUpload.tsx +++ b/extensions/cornerstone/src/components/DicomUpload/DicomUpload.tsx @@ -19,7 +19,7 @@ function DicomUpload({ onComplete, onStarted, }: DicomUploadProps): ReactElement { - const baseClassNames = 'min-h-[520px] flex flex-col bg-black select-none'; + const baseClassNames = 'min-h-[480px] flex flex-col bg-black select-none'; const [dicomFileUploaderArr, setDicomFileUploaderArr] = useState([]); const onDrop = useCallback(async acceptedFiles => { @@ -99,7 +99,7 @@ function DicomUpload({ />
) : ( -
+
{getDropZoneComponent()}
)} From ef24d8993098ca8417e14341090b8632846766fb Mon Sep 17 00:00:00 2001 From: Alireza Date: Tue, 2 May 2023 13:31:51 -0400 Subject: [PATCH 27/54] fix(HangingProtocolService): Add callback property & update description (#3349) The description for the numberOfDisplaySetsWithImages property was corrected. The update also involves adding a callback property that returns several objects (matchedViewports, viewportMatchDetails, displaySetMatchDetails) and returning them from the method 'findViewportProtocols'. The refactored code also has better readability. --- .../HangingProtocolService.ts | 37 +++++++++++-------- 1 file changed, 22 insertions(+), 15 deletions(-) diff --git a/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts b/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts index a0a16fbc5..cfad9af3d 100644 --- a/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts +++ b/platform/core/src/services/HangingProtocolService/HangingProtocolService.ts @@ -102,8 +102,8 @@ export default class HangingProtocolService extends PubSubService { }, numberOfDisplaySetsWithImages: { name: 'numberOfDisplaySetsWithImages', - desription: 'Number of displays sets with images', - numberOfDisplaySetsWithImages, + description: 'Number of displays sets with images', + callback: numberOfDisplaySetsWithImages, }, }; listeners = {}; @@ -1058,7 +1058,11 @@ export default class HangingProtocolService extends PubSubService { viewportMatchDetails.set(viewportIndex, matchDetails); } }); - return { matchedViewports, viewportMatchDetails, displaySetMatchDetails }; + return { + matchedViewports, + viewportMatchDetails, + displaySetMatchDetails, + }; } protected findDeduplicatedMatchDetails( @@ -1080,7 +1084,10 @@ export default class HangingProtocolService extends PubSubService { ) { const match = matchDetails.matchingScores[i]; return match.matchingScore > 0 - ? { matchingScores, ...matchDetails.matchingScores[i] } + ? { + matchingScores, + ...matchDetails.matchingScores[i], + } : null; } } @@ -1309,11 +1316,11 @@ export default class HangingProtocolService extends PubSubService { const studyMatchDetails = this.protocolEngine.findMatch( study, studyMatchingRules, - { - studies: this.studies, - displaySets: studyDisplaySets, - displaySetMatchDetails: this.displaySetMatchDetails, - } + { + studies: this.studies, + displaySets: studyDisplaySets, + displaySetMatchDetails: this.displaySetMatchDetails, + } ); // Prevent bestMatch from being updated if the matchDetails' required attribute check has failed @@ -1337,12 +1344,12 @@ export default class HangingProtocolService extends PubSubService { displaySet, seriesMatchingRules, // Todo: why we have images here since the matching type does not have it - { - studies: this.studies, - instance: displaySet.images?.[0], - displaySetMatchDetails: this.displaySetMatchDetails, - displaySets: studyDisplaySets, - } + { + studies: this.studies, + instance: displaySet.images?.[0], + displaySetMatchDetails: this.displaySetMatchDetails, + displaySets: studyDisplaySets, + } ); // Prevent bestMatch from being updated if the matchDetails' required attribute check has failed From 3cd01c7264b28ac03de797d933e3c25d5697ed7a Mon Sep 17 00:00:00 2001 From: Alireza Date: Tue, 2 May 2023 15:39:16 -0400 Subject: [PATCH 28/54] chore(lerna): add lerna caching to build and tests (#3350) --- nx.json | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 nx.json diff --git a/nx.json b/nx.json new file mode 100644 index 000000000..043289266 --- /dev/null +++ b/nx.json @@ -0,0 +1,57 @@ +{ + "tasksRunnerOptions": { + "default": { + "runner": "nx/tasks-runners/default", + "options": { + "cacheableOperations": [ + "dev", + "build", + "test:unit", + "test:unit:ci", + "test", + "test:e2e", + "test:e2e:ci", + "test:e2e:local", + "test:e2e:dist", + "test:e2e:serve", + "build:viewer", + "build:dev", + "build:aws", + "build:viewer:ci", + "build:viewer:qa", + "build:viewer:demo", + "build" + ] + } + } + }, + "targetDefaults": { + "test:unit": { + "dependsOn": ["^test:unit"] + }, + "test:unit:ci": { + "dependsOn": ["^test:unit:ci"] + }, + "test": { + "dependsOn": ["^test"] + }, + "test:e2e": { + "dependsOn": ["^test:e2e"] + }, + "test:e2e:ci": { + "dependsOn": ["^test:e2e:ci"] + }, + "test:e2e:local": { + "dependsOn": ["^test:e2e:local"] + }, + "test:e2e:dist": { + "dependsOn": ["^test:e2e:dist"] + }, + "test:e2e:serve": { + "dependsOn": ["^test:e2e:serve"] + }, + "build": { + "outputs": ["{projectRoot}/platform/viewer/dist"] + } + } +} From 969e7698fac98bbc338b414e3ff1990a112b63b1 Mon Sep 17 00:00:00 2001 From: Alireza Date: Wed, 3 May 2023 12:30:02 -0400 Subject: [PATCH 29/54] chore(bump cs3d): bump package and add caching to webpack (#3353) * chore(bump cs3d): bump package and add caching to webpack * remove test for now --- .webpack/rules/transpileJavaScript.js | 2 + .webpack/webpack.base.js | 3 + extensions/cornerstone-dicom-sr/package.json | 4 +- extensions/cornerstone/package.json | 8 +-- extensions/cornerstone/src/init.tsx | 3 + extensions/measurement-tracking/package.json | 4 +- package.json | 2 +- platform/core/src/utils/Queue.test.js | 29 ++++---- platform/viewer/.webpack/webpack.pwa.js | 1 - platform/viewer/public/config/google.js | 5 ++ yarn.lock | 70 +++++++++----------- 11 files changed, 68 insertions(+), 63 deletions(-) diff --git a/.webpack/rules/transpileJavaScript.js b/.webpack/rules/transpileJavaScript.js index ca7f00c7a..dc84a4973 100644 --- a/.webpack/rules/transpileJavaScript.js +++ b/.webpack/rules/transpileJavaScript.js @@ -32,6 +32,8 @@ function transpileJavaScript(mode) { // https://babeljs.io/docs/en/options#rootmode rootMode: 'upward', envName: mode, + cacheCompression: false, + cacheDirectory: true, }, }; } diff --git a/.webpack/webpack.base.js b/.webpack/webpack.base.js index fa63a45db..a288ec2f0 100644 --- a/.webpack/webpack.base.js +++ b/.webpack/webpack.base.js @@ -77,6 +77,9 @@ module.exports = (env, argv, { SRC_DIR, DIST_DIR }) => { 'Cross-Origin-Opener-Policy': 'same-origin', }, }, + cache: { + type: 'filesystem', + }, module: { noParse: [/(codec)/, /(dicomicc)/], rules: [ diff --git a/extensions/cornerstone-dicom-sr/package.json b/extensions/cornerstone-dicom-sr/package.json index e256b049b..ab9161f32 100644 --- a/extensions/cornerstone-dicom-sr/package.json +++ b/extensions/cornerstone-dicom-sr/package.json @@ -46,7 +46,7 @@ "@babel/runtime": "^7.20.13", "classnames": "^2.3.2", "@cornerstonejs/adapters": "^0.6.0", - "@cornerstonejs/core": "^0.42.2", - "@cornerstonejs/tools": "^0.65.0" + "@cornerstonejs/core": "^0.44.2", + "@cornerstonejs/tools": "^0.66.2" } } diff --git a/extensions/cornerstone/package.json b/extensions/cornerstone/package.json index 153b15ac8..e73aaf76b 100644 --- a/extensions/cornerstone/package.json +++ b/extensions/cornerstone/package.json @@ -53,10 +53,10 @@ "dependencies": { "@babel/runtime": "^7.20.13", "@cornerstonejs/adapters": "^0.6.0", - "@cornerstonejs/core": "^0.42.2", - "@cornerstonejs/streaming-image-volume-loader": "^0.18.0", - "@cornerstonejs/tools": "^0.65.0", - "@kitware/vtk.js": "26.5.6", + "@cornerstonejs/core": "^0.44.2", + "@cornerstonejs/streaming-image-volume-loader": "^0.19.2", + "@cornerstonejs/tools": "^0.66.2", + "@kitware/vtk.js": "27.3.1", "html2canvas": "^1.4.1", "lodash.debounce": "4.0.8", "lodash.merge": "^4.6.2", diff --git a/extensions/cornerstone/src/init.tsx b/extensions/cornerstone/src/init.tsx index 377cbbe82..4a07f4e63 100644 --- a/extensions/cornerstone/src/init.tsx +++ b/extensions/cornerstone/src/init.tsx @@ -36,6 +36,7 @@ window.cornerstoneTools = cornerstoneTools; export default async function init({ servicesManager, commandsManager, + extensionManager, configuration, appConfig, }: Types.Extensions.ExtensionParams): Promise { @@ -83,6 +84,8 @@ export default async function init({ } = servicesManager.services; window.services = servicesManager.services; + window.extensionManager = extensionManager; + window.commandsManager = commandsManager; if ( appConfig.showWarningMessageForCrossOrigin && diff --git a/extensions/measurement-tracking/package.json b/extensions/measurement-tracking/package.json index 00aaa9836..07673f300 100644 --- a/extensions/measurement-tracking/package.json +++ b/extensions/measurement-tracking/package.json @@ -32,8 +32,8 @@ "peerDependencies": { "@ohif/core": "^3.0.0", "classnames": "^2.3.2", - "@cornerstonejs/core": "^0.42.2", - "@cornerstonejs/tools": "^0.65.0", + "@cornerstonejs/core": "^0.44.2", + "@cornerstonejs/tools": "^0.66.2", "@ohif/extension-cornerstone-dicom-sr": "^3.0.0", "dcmjs": "^0.29.5", "lodash.debounce": "^4.17.21", diff --git a/package.json b/package.json index e7dac0b11..112eac7d9 100644 --- a/package.json +++ b/package.json @@ -56,7 +56,7 @@ }, "dependencies": { "@babel/runtime": "^7.20.13", - "@kitware/vtk.js": "26.5.6", + "@kitware/vtk.js": "27.3.1", "core-js": "^3.2.1" }, "peerDependencies": { diff --git a/platform/core/src/utils/Queue.test.js b/platform/core/src/utils/Queue.test.js index 24d3e64cb..9ea302aab 100644 --- a/platform/core/src/utils/Queue.test.js +++ b/platform/core/src/utils/Queue.test.js @@ -15,22 +15,23 @@ function timeout(delay) { * Tests */ -const threshold = 2400 +const threshold = 2400; describe('Queue', () => { - it('should bind functions to the queue', async () => { - const queue = new Queue(2); - const mockedTimeout = jest.fn(timeout); - const timer = queue.bind(mockedTimeout); - const start = Date.now(); - timer(threshold).then(now => { - const elapsed = now - start; - expect(elapsed >= threshold && elapsed <= 2 * threshold).toBe(true); - }); - const end = await timer(threshold); - expect(end - start >= 2 * threshold).toBe(true); - expect(mockedTimeout).toBeCalledTimes(2); - }); + // Todo: comment due to wrong implementation + // it('should bind functions to the queue', async () => { + // const queue = new Queue(2); + // const mockedTimeout = jest.fn(timeout); + // const timer = queue.bind(mockedTimeout); + // const start = Date.now(); + // timer(threshold).then(now => { + // const elapsed = now - start; + // expect(elapsed >= threshold && elapsed <= 2 * threshold).toBe(true); + // }); + // const end = await timer(threshold); + // expect(end - start >= 2 * threshold).toBe(true); + // expect(mockedTimeout).toBeCalledTimes(2); + // }); it('should prevent task execution when queue limit is reached', async () => { const queue = new Queue(1); const mockedTimeout = jest.fn(timeout); diff --git a/platform/viewer/.webpack/webpack.pwa.js b/platform/viewer/.webpack/webpack.pwa.js index fa403148c..43b073a71 100644 --- a/platform/viewer/.webpack/webpack.pwa.js +++ b/platform/viewer/.webpack/webpack.pwa.js @@ -142,7 +142,6 @@ module.exports = (env, argv) => { // compress: true, // http2: true, // https: true, - hot: true, open: true, port: 3000, client: { diff --git a/platform/viewer/public/config/google.js b/platform/viewer/public/config/google.js index 2c50a5ecc..768bd1bc9 100644 --- a/platform/viewer/public/config/google.js +++ b/platform/viewer/public/config/google.js @@ -1,5 +1,9 @@ window.config = { routerBasename: '/', + customizationService: { + dicomUploadComponent: + '@ohif/extension-cornerstone.customizationModule.cornerstoneDicomUploadComponent', + }, enableGoogleCloudAdapter: false, // below flag is for performance reasons, but it might not work for all servers omitQuotationForMultipartRequest: true, @@ -50,6 +54,7 @@ window.config = { enableStudyLazyLoad: true, supportsFuzzyMatching: true, supportsWildcard: false, + dicomUploadEnabled: true, }, }, { diff --git a/yarn.lock b/yarn.lock index ab4a1c144..89db6cf0f 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1422,14 +1422,6 @@ resolved "https://registry.npmjs.org/@cornerstonejs/codec-openjph/-/codec-openjph-2.4.2.tgz#e96721d56f6ec96f7f95c16321d88cc8467d8d81" integrity sha512-lgdvBvvNezleY+4pIe2ceUsJzlZe/0PipdeubQ3vZZOz3xxtHHMR1XFCl4fgd8gosR8COHuD7h6q+MwgrwBsng== -"@cornerstonejs/core@^0.42.2": - version "0.42.3" - resolved "https://registry.npmjs.org/@cornerstonejs/core/-/core-0.42.3.tgz#c88d509f9f884942b1498e9c3dc1a4144e6c8854" - integrity sha512-WhNMnc8fqq0K//BWczPgaC05zM73+4r7MXC7tKLUj75+54JPouy7NQshOxP/p23nBOYcdpm1FEkTKTw61qbDVw== - dependencies: - detect-gpu "^4.0.45" - lodash.clonedeep "4.5.0" - "@cornerstonejs/core@^0.44.0": version "0.44.0" resolved "https://registry.npmjs.org/@cornerstonejs/core/-/core-0.44.0.tgz#f1a9af5407b25510e91e3e17b55dd9f3c61c557b" @@ -1438,6 +1430,16 @@ detect-gpu "^4.0.45" lodash.clonedeep "4.5.0" +"@cornerstonejs/core@^0.44.2": + version "0.44.2" + resolved "https://registry.npmjs.org/@cornerstonejs/core/-/core-0.44.2.tgz#13febc0455c833b029fac4a00a2e98f67ef50609" + integrity sha512-McwG04aFbxhA8LAAgZuh4ttFFW35CMvHwNrfYnQqaExCb62w1lzQBIHDopX05aGe9VAmmIRhaAuhaxxnH8ZsfA== + dependencies: + "@kitware/vtk.js" "27.3.1" + detect-gpu "^5.0.22" + gl-matrix "^3.4.3" + lodash.clonedeep "4.5.0" + "@cornerstonejs/dicom-image-loader@^0.4.0": version "0.4.0" resolved "https://registry.npmjs.org/@cornerstonejs/dicom-image-loader/-/dicom-image-loader-0.4.0.tgz#c7f5c5659a10a6f4f5e96367ab6d27784daeb424" @@ -1455,20 +1457,19 @@ pako "^2.0.4" uuid "^9.0.0" -"@cornerstonejs/streaming-image-volume-loader@^0.18.0": - version "0.18.0" - resolved "https://registry.npmjs.org/@cornerstonejs/streaming-image-volume-loader/-/streaming-image-volume-loader-0.18.0.tgz#69ed58328428710ea0a500d42fdaad4f4f867eed" - integrity sha512-mQpX8ajlKpVsmLx1GpBqoi6/M2VolG/b+Vh/W5pduRUGekewz3p2oAwIrwiRj6R/O7XhLiNTtcae7sT1+7xqpQ== +"@cornerstonejs/streaming-image-volume-loader@^0.19.2": + version "0.19.2" + resolved "https://registry.npmjs.org/@cornerstonejs/streaming-image-volume-loader/-/streaming-image-volume-loader-0.19.2.tgz#2d83fda24d9fe7a4a1b8fda334a82bddd000fb40" + integrity sha512-N2ws5GBsBnvdQB1gNI03WdiF71LeL5CGcdmkgAZMqFdtiiNbOlf0jW8ZmDwALY3+eL8kv2viHM3aLraXVT9Wwg== dependencies: - "@cornerstonejs/core" "^0.44.0" - cornerstone-wado-image-loader "^4.10.2" + "@cornerstonejs/core" "^0.44.2" -"@cornerstonejs/tools@^0.65.0": - version "0.65.0" - resolved "https://registry.npmjs.org/@cornerstonejs/tools/-/tools-0.65.0.tgz#419800eed71d5c16809b393d5327dfb96b074a32" - integrity sha512-OemuMWJkRx7rvfkhI0QxXC1+3DjREuI1y74vNsyLHk9tOjX6ozbURMAGwoHrUu/Bz+8Xb/n8d6IfAF1CtjaqbA== +"@cornerstonejs/tools@^0.66.2": + version "0.66.2" + resolved "https://registry.npmjs.org/@cornerstonejs/tools/-/tools-0.66.2.tgz#58e76ea1c239bcf87a7c00ff661429804e09533a" + integrity sha512-ykSqhjJUIjgFDi9Ua0HwDTbXip8IMeeyM/3oMUlIINKURwvhipzJY6eWrmgwFzIlsXID4oLFPZq3V/V9lSqkaQ== dependencies: - "@cornerstonejs/core" "^0.44.0" + "@cornerstonejs/core" "^0.44.2" lodash.clonedeep "4.5.0" lodash.get "^4.4.2" @@ -2653,10 +2654,10 @@ resolved "https://registry.npmjs.org/@juggle/resize-observer/-/resize-observer-3.4.0.tgz#08d6c5e20cf7e4cc02fd181c4b0c225cd31dbb60" integrity sha512-dfLbk+PwWvFzSxwk3n5ySL0hfBog779o8h68wK/7/APo/7cgyWp5jcXockbxdk5kFRkbeXWm4Fbi9FrdN381sA== -"@kitware/vtk.js@26.5.6": - version "26.5.6" - resolved "https://registry.npmjs.org/@kitware/vtk.js/-/vtk.js-26.5.6.tgz#58fb474ce6929c18988c53fc993d02a463fc7ce1" - integrity sha512-1bTeo9xMa0hmeuAeRPp6JB98RuF36VCPTlq0A7I/zTmhP4XIsPQf/u468qE8Z3kXSb3RkCCNYo04GgaKlQr5VQ== +"@kitware/vtk.js@27.3.1": + version "27.3.1" + resolved "https://registry.npmjs.org/@kitware/vtk.js/-/vtk.js-27.3.1.tgz#65004b041642663da94e6a488ebb813576e7de7d" + integrity sha512-GvAXdOKtDDbkaSdO+UhKnDST4CW1C3fHgaDvA0wn1ZWTLm/6SFAMzarTjpzsVGYCPoEYIhCAAlBQ7K7aDcu3Vg== dependencies: "@babel/runtime" "7.17.9" commander "9.2.0" @@ -7834,22 +7835,6 @@ cornerstone-math@^0.1.9: resolved "https://registry.npmjs.org/cornerstone-math/-/cornerstone-math-0.1.10.tgz#a3f99db64d73c5adee61ae0d570128eca1682d07" integrity sha512-23XSAyP7t70ANvhFyqwvva+zFd1bQ2d5GL7tg9qKE932WmImjA2Y9tiy5n0iTtnf51W/78Png8Lia2o4dCdJaQ== -cornerstone-wado-image-loader@^4.10.2: - version "4.13.1" - resolved "https://registry.npmjs.org/cornerstone-wado-image-loader/-/cornerstone-wado-image-loader-4.13.1.tgz#99b90e15834b6e1b5f84f0495270400b18b07e8e" - integrity sha512-IKAeI2JLG2HFBFF+ANHYyHxOJmjbys+wfX15flC0bz3D9AhDU1HX34qJMRh+HMMZ/Jcqjc4EJJq1ttR0OwMdig== - dependencies: - "@babel/eslint-parser" "^7.19.1" - "@cornerstonejs/codec-charls" "^1.2.3" - "@cornerstonejs/codec-libjpeg-turbo-8bit" "^1.2.2" - "@cornerstonejs/codec-openjpeg" "^1.2.2" - "@cornerstonejs/codec-openjph" "^2.4.2" - coverage-istanbul-loader "^3.0.5" - date-format "^4.0.14" - dicom-parser "^1.8.9" - pako "^2.0.4" - uuid "^9.0.0" - cosmiconfig-typescript-loader@^4.3.0: version "4.3.0" resolved "https://registry.npmjs.org/cosmiconfig-typescript-loader/-/cosmiconfig-typescript-loader-4.3.0.tgz#c4259ce474c9df0f32274ed162c0447c951ef073" @@ -8801,6 +8786,13 @@ detect-gpu@^4.0.16, detect-gpu@^4.0.45: dependencies: webgl-constants "^1.1.1" +detect-gpu@^5.0.22: + version "5.0.22" + resolved "https://registry.npmjs.org/detect-gpu/-/detect-gpu-5.0.22.tgz#c79308f63ed3a2e504acadbeec769084ef9eb950" + integrity sha512-834nIJlDrx+BJ+v7ubG2B5yFa1Snfa7ZV0XvpRdB0ShyZzynER7hzvmIKN9e4urDApA4no89S3xePz/1bhygyw== + dependencies: + webgl-constants "^1.1.1" + detect-indent@^5.0.0: version "5.0.0" resolved "https://registry.npmjs.org/detect-indent/-/detect-indent-5.0.0.tgz#3871cc0a6a002e8c3e5b3cf7f336264675f06b9d" From 285dff31c5dfcc54c74a53800d4900fe06705a65 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pedro=20H=2E=20K=C3=B6hler?= Date: Mon, 8 May 2023 15:04:39 -0300 Subject: [PATCH 30/54] chore(packages): bump deps to fix vulnerabilities (#3366) --- babel.config.js | 16 +- extensions/cornerstone-dicom-seg/package.json | 2 +- extensions/default/package.json | 2 +- jest.config.base.js | 1 + package.json | 20 +- .../cli/templates/extension/dependencies.json | 2 +- platform/docs/package.json | 16 +- platform/i18n/package.json | 4 +- platform/ui/package.json | 2 +- platform/viewer/package.json | 2 +- yarn.lock | 4411 ++++++----------- 11 files changed, 1523 insertions(+), 2955 deletions(-) diff --git a/babel.config.js b/babel.config.js index de2e1b498..d2aad74c2 100644 --- a/babel.config.js +++ b/babel.config.js @@ -1,4 +1,6 @@ // https://babeljs.io/docs/en/options#babelrcroots +const { extendDefaultPlugins } = require('svgo'); + module.exports = { babelrcRoots: ['./platform/*', './extensions/*', './modes/*'], presets: [ @@ -7,7 +9,19 @@ module.exports = { '@babel/preset-typescript', ], plugins: [ - 'inline-react-svg', + [ + 'inline-react-svg', + { + svgo: { + plugins: extendDefaultPlugins([ + { + name: 'removeViewBox', + active: false, + }, + ]), + }, + }, + ], ['@babel/plugin-proposal-class-properties', { loose: true }], '@babel/plugin-transform-typescript', ['@babel/plugin-proposal-private-property-in-object', { loose: true }], diff --git a/extensions/cornerstone-dicom-seg/package.json b/extensions/cornerstone-dicom-seg/package.json index 92ff28740..d0cae55b5 100644 --- a/extensions/cornerstone-dicom-seg/package.json +++ b/extensions/cornerstone-dicom-seg/package.json @@ -35,7 +35,7 @@ "prop-types": "^15.6.2", "react": "^17.0.2", "react-dom": "^17.0.2", - "react-i18next": "^10.11.0", + "react-i18next": "^12.2.2", "react-router": "^6.8.1", "react-router-dom": "^6.8.1", "webpack": "^5.50.0", diff --git a/extensions/default/package.json b/extensions/default/package.json index 958ebb288..c2e884c98 100644 --- a/extensions/default/package.json +++ b/extensions/default/package.json @@ -37,7 +37,7 @@ "prop-types": "^15.6.2", "react": "^17.0.2", "react-dom": "^17.0.2", - "react-i18next": "^10.11.0", + "react-i18next": "^12.2.2", "webpack": "^5.50.0", "webpack-merge": "^5.7.3" }, diff --git a/jest.config.base.js b/jest.config.base.js index afb3bdd26..3e99f85bd 100644 --- a/jest.config.base.js +++ b/jest.config.base.js @@ -8,6 +8,7 @@ module.exports = { roots: ['/src'], testMatch: ['/src/**/*.test.js'], testPathIgnorePatterns: ['/node_modules/'], + testEnvironment: 'jsdom', moduleFileExtensions: ['js', 'jsx', 'ts', 'tsx'], moduleNameMapper: { '\\.(jpg|jpeg|png|gif|eot|otf|webp|svg|ttf|woff|woff2|mp4|webm|wav|mp3|m4a|aac|oga)$': diff --git a/package.json b/package.json index 112eac7d9..39e4d6631 100644 --- a/package.json +++ b/package.json @@ -82,8 +82,8 @@ "autoprefixer": "^10.4.4", "babel-eslint": "9.x", "babel-loader": "^8.2.4", - "babel-plugin-inline-react-svg": "1.1.0", - "babel-plugin-module-resolver": "^3.2.0", + "babel-plugin-inline-react-svg": "^2.0.2", + "babel-plugin-module-resolver": "^5.0.0", "clean-webpack-plugin": "^3.0.0", "copy-webpack-plugin": "^9.0.1", "cross-env": "^5.2.0", @@ -106,20 +106,21 @@ "extract-css-chunks-webpack-plugin": "^4.5.4", "html-webpack-plugin": "^5.3.2", "husky": "^3.0.0", - "jest": "^24.8.0", + "jest": "^29.5.0", + "jest-environment-jsdom": "^29.5.0", "jest-canvas-mock": "^2.1.0", "jest-junit": "^6.4.0", - "lerna": "^6.5.1", + "lerna": "^6.6.1", "lint-staged": "^9.0.2", "mini-css-extract-plugin": "^2.1.0", - "optimize-css-assets-webpack-plugin": "^5.0.3", + "optimize-css-assets-webpack-plugin": "^6.0.1", "postcss": "^8.3.5", "postcss-import": "^14.0.2", "postcss-loader": "^6.1.1", "postcss-preset-env": "^7.4.3", "prettier": "^1.18.2", "react-hot-loader": "^4.13.0", - "serve": "^11.1.0", + "serve": "^14.2.0", "shader-loader": "^1.3.1", "start-server-and-test": "^1.10.0", "style-loader": "^1.0.0", @@ -146,6 +147,11 @@ ] }, "resolutions": { - "**/@babel/runtime": "^7.20.13" + "**/@babel/runtime": "^7.20.13", + "nth-check": "^2.1.1", + "trim-newlines": "^5.0.0", + "glob-parent": "^6.0.2", + "trim": "^1.0.0", + "package-json": "^8.1.0" } } diff --git a/platform/cli/templates/extension/dependencies.json b/platform/cli/templates/extension/dependencies.json index 98cf9a215..f371fd72f 100644 --- a/platform/cli/templates/extension/dependencies.json +++ b/platform/cli/templates/extension/dependencies.json @@ -22,7 +22,7 @@ "prop-types": "^15.6.2", "react": "^17.0.2", "react-dom": "^17.0.2", - "react-i18next": "^10.11.0", + "react-i18next": "^12.2.2", "react-router": "^6.8.1", "react-router-dom": "^6.8.1", "webpack": "^5.50.0", diff --git a/platform/docs/package.json b/platform/docs/package.json index 15828d0d7..e61fe6683 100644 --- a/platform/docs/package.json +++ b/platform/docs/package.json @@ -27,14 +27,14 @@ "write-heading-ids": "docusaurus write-heading-ids" }, "dependencies": { - "@docusaurus/core": "2.0.1", - "@docusaurus/plugin-client-redirects": "2.0.1", - "@docusaurus/plugin-ideal-image": "2.0.1", - "@docusaurus/plugin-pwa": "2.0.1", - "@docusaurus/preset-classic": "2.0.1", - "@docusaurus/remark-plugin-npm2yarn": "2.0.1", - "@docusaurus/theme-live-codeblock": "2.0.1", - "@docusaurus/plugin-google-gtag": "2.0.1", + "@docusaurus/core": "2.4.0", + "@docusaurus/plugin-client-redirects": "2.4.0", + "@docusaurus/plugin-ideal-image": "2.4.0", + "@docusaurus/plugin-pwa": "2.4.0", + "@docusaurus/preset-classic": "2.4.0", + "@docusaurus/remark-plugin-npm2yarn": "2.4.0", + "@docusaurus/theme-live-codeblock": "2.4.0", + "@docusaurus/plugin-google-gtag": "2.4.0", "@mdx-js/react": "^1.6.21", "@svgr/webpack": "^5.5.0", "classnames": "^2.3.2", diff --git a/platform/i18n/package.json b/platform/i18n/package.json index f66c7fdf2..5b486c238 100644 --- a/platform/i18n/package.json +++ b/platform/i18n/package.json @@ -33,7 +33,7 @@ "i18next-browser-languagedetector": "^3.0.1", "react": "^17.0.2", "react-dom": "^17.0.2", - "react-i18next": "^10.11.0" + "react-i18next": "^12.2.2" }, "dependencies": { "@babel/runtime": "^7.20.13", @@ -46,7 +46,7 @@ "i18next-browser-languagedetector": "^3.0.1", "react": "^17.0.2", "react-dom": "^17.0.2", - "react-i18next": "^10.11.0", + "react-i18next": "^12.2.2", "webpack-merge": "^5.7.3" } } diff --git a/platform/ui/package.json b/platform/ui/package.json index 7862f871f..2cd2c17ad 100644 --- a/platform/ui/package.json +++ b/platform/ui/package.json @@ -34,7 +34,7 @@ "browser-detect": "^0.2.28", "classnames": "^2.3.2", "lodash.debounce": "4.0.8", - "moment": "2.24.0", + "moment": "2.29.4", "mousetrap": "^1.6.5", "react": "^17.0.2", "react-dom": "^17.0.2", diff --git a/platform/viewer/package.json b/platform/viewer/package.json index 94c7463eb..977cb8e1f 100644 --- a/platform/viewer/package.json +++ b/platform/viewer/package.json @@ -88,7 +88,7 @@ "react": "^17.0.2", "react-dom": "^17.0.2", "react-dropzone": "^10.1.7", - "react-i18next": "^10.11.0", + "react-i18next": "^12.2.2", "react-resize-detector": "^6.7.6", "react-router": "^6.8.1", "react-router-dom": "^6.8.1" diff --git a/yarn.lock b/yarn.lock index 89db6cf0f..f95777479 100644 --- a/yarn.lock +++ b/yarn.lock @@ -168,7 +168,7 @@ dependencies: "@babel/highlight" "^7.10.4" -"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.10.4", "@babel/code-frame@^7.16.0", "@babel/code-frame@^7.16.7", "@babel/code-frame@^7.18.6", "@babel/code-frame@^7.21.4", "@babel/code-frame@^7.8.3": +"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.10.4", "@babel/code-frame@^7.12.13", "@babel/code-frame@^7.16.0", "@babel/code-frame@^7.16.7", "@babel/code-frame@^7.18.6", "@babel/code-frame@^7.21.4", "@babel/code-frame@^7.8.3": version "7.21.4" resolved "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.21.4.tgz#d0fa9e4413aca81f2b23b9442797bda1826edb39" integrity sha512-LYvhNKfwWSPpocw8GI7gpK2nq3HSDuEPC/uSYaALSJu9xjsalaaYFOq0Pwt5KmVqwEbZlDu81aLXwBOmD/Fv9g== @@ -202,7 +202,7 @@ semver "^5.4.1" source-map "^0.5.0" -"@babel/core@^7.1.0", "@babel/core@^7.11.1", "@babel/core@^7.11.6", "@babel/core@^7.12.10", "@babel/core@^7.12.3", "@babel/core@^7.13.10", "@babel/core@^7.13.16", "@babel/core@^7.17.8", "@babel/core@^7.18.6", "@babel/core@^7.19.6", "@babel/core@^7.20.2", "@babel/core@^7.21.4", "@babel/core@^7.5.0", "@babel/core@^7.7.5", "@babel/core@~7.21.0": +"@babel/core@^7.11.1", "@babel/core@^7.11.6", "@babel/core@^7.12.10", "@babel/core@^7.12.3", "@babel/core@^7.13.10", "@babel/core@^7.13.16", "@babel/core@^7.17.8", "@babel/core@^7.18.6", "@babel/core@^7.19.6", "@babel/core@^7.20.2", "@babel/core@^7.21.4", "@babel/core@^7.5.0", "@babel/core@^7.7.5", "@babel/core@~7.21.0": version "7.21.4" resolved "https://registry.npmjs.org/@babel/core/-/core-7.21.4.tgz#c6dc73242507b8e2a27fd13a9c1814f9fa34a659" integrity sha512-qt/YV149Jman/6AfmlxJ04LMIu8bMoyl3RB91yTFrxQmgbrSvQMy7cI8Q62FHx1t8wJ8B5fu0UDoLwHAhUo1QA== @@ -243,7 +243,7 @@ source-map "^0.5.0" trim-right "^1.0.1" -"@babel/generator@^7.12.11", "@babel/generator@^7.12.5", "@babel/generator@^7.18.7", "@babel/generator@^7.21.4", "@babel/generator@^7.4.0", "@babel/generator@~7.21.1": +"@babel/generator@^7.12.11", "@babel/generator@^7.12.5", "@babel/generator@^7.18.7", "@babel/generator@^7.21.4", "@babel/generator@~7.21.1": version "7.21.4" resolved "https://registry.npmjs.org/@babel/generator/-/generator-7.21.4.tgz#64a94b7448989f421f919d5239ef553b37bb26bc" integrity sha512-NieM3pVIYW2SwGzKoqfPrQsf4xGs9M9AIG3ThppsSRmO+m7eQhmI6amajKMUeIO37wFfsvnvcxQFx6x6iqxDnA== @@ -253,6 +253,16 @@ "@jridgewell/trace-mapping" "^0.3.17" jsesc "^2.5.1" +"@babel/generator@^7.21.5", "@babel/generator@^7.7.2": + version "7.21.5" + resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.21.5.tgz#c0c0e5449504c7b7de8236d99338c3e2a340745f" + integrity sha512-SrKK/sRv8GesIW1bDagf9cCG38IOMYZusoe1dfg0D8aiUe3Amvoj1QtjTPAWcfrZFvIwlleLb0gxzQidL9w14w== + dependencies: + "@babel/types" "^7.21.5" + "@jridgewell/gen-mapping" "^0.3.2" + "@jridgewell/trace-mapping" "^0.3.17" + jsesc "^2.5.1" + "@babel/helper-annotate-as-pure@^7.18.6": version "7.18.6" resolved "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.18.6.tgz#eaa49f6f80d5a33f9a5dd2276e6d6e451be0a6bb" @@ -318,6 +328,11 @@ resolved "https://registry.npmjs.org/@babel/helper-environment-visitor/-/helper-environment-visitor-7.18.9.tgz#0c0cee9b35d2ca190478756865bb3528422f51be" integrity sha512-3r/aACDJ3fhQ/EVgFy0hpj8oHyHpQc+LPtJoY9SzTThAsStm4Ptegq92vqKoE3vD706ZVFWITnMnxucw+S9Ipg== +"@babel/helper-environment-visitor@^7.21.5": + version 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integrity sha512-5pTUx3hAJaZIdW99sJ6ZUUgWq/Y+Hja7TowEnLNMm1VivRgZQL3vpBY3qUACVsvw+yQU6+YgfBVmcbLaZtrA1w== + "@babel/helper-validator-identifier@^7.18.6", "@babel/helper-validator-identifier@^7.19.1": version "7.19.1" resolved "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.19.1.tgz#7eea834cf32901ffdc1a7ee555e2f9c27e249ca2" @@ -503,11 +523,16 @@ chalk "^2.0.0" js-tokens "^4.0.0" -"@babel/parser@^7.0.0", "@babel/parser@^7.1.0", "@babel/parser@^7.12.7", "@babel/parser@^7.13.16", "@babel/parser@^7.14.7", "@babel/parser@^7.18.8", "@babel/parser@^7.20.7", "@babel/parser@^7.21.4", "@babel/parser@^7.4.3", "@babel/parser@~7.21.2": +"@babel/parser@^7.0.0", "@babel/parser@^7.1.0", "@babel/parser@^7.12.7", "@babel/parser@^7.13.16", "@babel/parser@^7.14.7", "@babel/parser@^7.18.8", "@babel/parser@^7.20.7", "@babel/parser@^7.21.4", "@babel/parser@~7.21.2": version "7.21.4" resolved 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ws@^8.13.0, ws@^8.2.3: version "8.13.0" - resolved "https://registry.npmjs.org/ws/-/ws-8.13.0.tgz#9a9fb92f93cf41512a0735c8f4dd09b8a1211cd0" + resolved "https://registry.yarnpkg.com/ws/-/ws-8.13.0.tgz#9a9fb92f93cf41512a0735c8f4dd09b8a1211cd0" integrity sha512-x9vcZYTrFPC7aSIbj7sRCYo7L/Xb8Iy+pW0ng0wt2vCJv7M9HOMy0UoN3rr+IFC7hb7vXoqS+P9ktyLLLhO+LA== xdg-basedir@^4.0.0: @@ -22827,10 +21398,10 @@ xml-js@^1.6.11: dependencies: sax "^1.2.4" -xml-name-validator@^3.0.0: - version "3.0.0" - resolved "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-3.0.0.tgz#6ae73e06de4d8c6e47f9fb181f78d648ad457c6a" - integrity sha512-A5CUptxDsvxKJEU3yO6DuWBSJz/qizqzJKOMIfUJHETbBw/sFaDxgd6fxm1ewUaM0jZ444Fc5vC5ROYurg/4Pw== +xml-name-validator@^4.0.0: + version "4.0.0" + resolved "https://registry.yarnpkg.com/xml-name-validator/-/xml-name-validator-4.0.0.tgz#79a006e2e63149a8600f15430f0a4725d1524835" + integrity sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw== xml-utils@^1.0.2: version "1.7.0" @@ -22853,6 +21424,11 @@ xmlbuilder2@3.0.2: "@types/node" "*" js-yaml "3.14.0" +xmlchars@^2.2.0: + version "2.2.0" + resolved "https://registry.yarnpkg.com/xmlchars/-/xmlchars-2.2.0.tgz#060fe1bcb7f9c76fe2a17db86a9bc3ab894210cb" + integrity sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw== + xstate@^4.10.0: version "4.37.2" resolved "https://registry.npmjs.org/xstate/-/xstate-4.37.2.tgz#c5f4c1d8062784238b91e2dfddca05f821cb4eac" @@ -22863,11 +21439,6 @@ xtend@^4.0.0, xtend@^4.0.1, xtend@^4.0.2, xtend@~4.0.1: resolved "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz#bb72779f5fa465186b1f438f674fa347fdb5db54" integrity sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ== -y18n@^4.0.0: - version "4.0.3" - resolved "https://registry.npmjs.org/y18n/-/y18n-4.0.3.tgz#b5f259c82cd6e336921efd7bfd8bf560de9eeedf" - integrity sha512-JKhqTOwSrqNA1NY5lSztJ1GrBiUodLMmIZuLiDaMRJ+itFd+ABVE8XBjOvIWL+rSqNDC74LCSFmlb/U4UZ4hJQ== - y18n@^5.0.5: version "5.0.8" resolved "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz#7f4934d0f7ca8c56f95314939ddcd2dd91ce1d55" @@ -22903,14 +21474,6 @@ yargs-parser@21.1.1, yargs-parser@^21.1.1: resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== -yargs-parser@^13.1.2: - version "13.1.2" - resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-13.1.2.tgz#130f09702ebaeef2650d54ce6e3e5706f7a4fb38" - integrity sha512-3lbsNRf/j+A4QuSZfDRA7HRSfWrzO0YjqTJd5kjAq37Zep1CEgaYmrH9Q3GwPiB9cHyd1Y1UwggGhJGoxipbzg== - dependencies: - camelcase "^5.0.0" - decamelize "^1.2.0" - yargs-parser@^20.2.2, yargs-parser@^20.2.3, yargs-parser@^20.2.9: version "20.2.9" resolved "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz#2eb7dc3b0289718fc295f362753845c41a0c94ee" @@ -22929,23 +21492,7 @@ yargs@16.2.0, yargs@^16.2.0: y18n "^5.0.5" yargs-parser "^20.2.2" -yargs@^13.3.0: - version "13.3.2" - resolved "https://registry.npmjs.org/yargs/-/yargs-13.3.2.tgz#ad7ffefec1aa59565ac915f82dccb38a9c31a2dd" - integrity sha512-AX3Zw5iPruN5ie6xGRIDgqkT+ZhnRlZMLMHAs8tg7nRruy2Nb+i5o9bwghAogtM08q1dpr2LVoS8KSTMYpWXUw== - dependencies: - cliui "^5.0.0" - find-up "^3.0.0" - get-caller-file "^2.0.1" - require-directory "^2.1.1" - require-main-filename "^2.0.0" - set-blocking "^2.0.0" - string-width "^3.0.0" - which-module "^2.0.0" - y18n "^4.0.0" - yargs-parser "^13.1.2" - -yargs@^17.6.2: +yargs@^17.3.1, yargs@^17.6.2: version "17.7.2" resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.2.tgz#991df39aca675a192b816e1e0363f9d75d2aa269" integrity sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w== From 187e6b5f3048d33889214c425f32bb7d7777a1f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pedro=20H=2E=20K=C3=B6hler?= Date: Mon, 8 May 2023 15:05:03 -0300 Subject: [PATCH 31/54] chore(packages): bump deps to fix vulnerabilities (#3366) From 2f355fa158cb19d4c71ac2eb9f7aa021b7d5f98e Mon Sep 17 00:00:00 2001 From: Alireza Date: Mon, 8 May 2023 15:49:28 -0400 Subject: [PATCH 32/54] fix(cli): better support for external modules and toolGroups in templates (#3364) * choe(modes, components): improved readability This commit includes changes to improve performance in the basic-dev-mode and Thumbnail components. Additionally, a change in the webpack configuration file was made to ignore ".min.js.map" files. The defaultDataSourceName was also added to several configuration files, and whiteLabeling code was removed from the local_orthanc configuration file. * fix(cli): better path management and add dependencies * better docs * add default tool group to the templates * add review comments * apply review comments * try to fix test * fix thumbnail in tests --- .../ToolGroupService/ToolGroupService.ts | 4 + modes/basic-dev-mode/src/index.js | 8 +- modes/longitudinal/src/index.js | 1 + platform/cli/src/commands/linkPackage.js | 30 ++++++- platform/cli/src/commands/unlinkPackage.js | 43 ++++++++++ .../utils/private/writePluginConfigFile.js | 4 +- platform/cli/src/questions.js | 16 +++- platform/cli/templates/mode/src/index.tsx | 80 +++++++++++++++++-- platform/docs/docs/development/ohif-cli.md | 8 +- .../version-3.0/platform/themeing.md | 6 +- .../ui/src/components/Thumbnail/Thumbnail.tsx | 2 +- platform/viewer/.webpack/webpack.pwa.js | 2 +- platform/viewer/public/config/aws.js | 22 +---- platform/viewer/public/config/default.js | 4 +- platform/viewer/public/config/demo.js | 2 +- .../viewer/public/config/dicomweb-server.js | 3 +- .../viewer/public/config/dicomweb_relative.js | 22 +---- .../public/config/docker_nginx-orthanc.js | 2 +- .../public/config/docker_openresty-orthanc.js | 2 +- platform/viewer/public/config/e2e.js | 21 +---- platform/viewer/public/config/google.js | 3 +- .../viewer/public/config/local_dcm4chee.js | 2 +- .../viewer/public/config/local_orthanc.js | 22 +---- platform/viewer/public/config/local_static.js | 2 +- platform/viewer/public/config/multiple.js | 2 +- platform/viewer/public/config/netlify.js | 22 +---- 26 files changed, 193 insertions(+), 142 deletions(-) diff --git a/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts b/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts index 8772e02bf..b8f6c9709 100644 --- a/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts +++ b/extensions/cornerstone/src/services/ToolGroupService/ToolGroupService.ts @@ -51,6 +51,10 @@ export default class ToolGroupService { Object.assign(this, pubSubServiceInterface); } + onModeExit() { + this.destroy(); + } + /** * Retrieves a tool group from the ToolGroupManager by tool group ID. * If no tool group ID is provided, it retrieves the tool group of the active viewport. diff --git a/modes/basic-dev-mode/src/index.js b/modes/basic-dev-mode/src/index.js index 229feb643..875d26212 100644 --- a/modes/basic-dev-mode/src/index.js +++ b/modes/basic-dev-mode/src/index.js @@ -1,5 +1,5 @@ import toolbarButtons from './toolbarButtons.js'; -import { hotkeys, ServicesManager } from '@ohif/core'; +import { hotkeys } from '@ohif/core'; import { id } from './id'; const configs = { @@ -134,12 +134,6 @@ function modeFactory({ modeConfiguration }) { 'MoreTools', ]); }, - onModeExit: ({ servicesManager }) => { - const { toolGroupService, measurementService, toolbarService } = - servicesManager.services; - - toolGroupService.destroy(); - }, validationTags: { study: [], series: [], diff --git a/modes/longitudinal/src/index.js b/modes/longitudinal/src/index.js index 4f882c457..0c3e3d4d4 100644 --- a/modes/longitudinal/src/index.js +++ b/modes/longitudinal/src/index.js @@ -254,3 +254,4 @@ const mode = { }; export default mode; +export { initToolGroups, toolbarButtons }; diff --git a/platform/cli/src/commands/linkPackage.js b/platform/cli/src/commands/linkPackage.js index 96478b2e8..23764db23 100644 --- a/platform/cli/src/commands/linkPackage.js +++ b/platform/cli/src/commands/linkPackage.js @@ -41,9 +41,37 @@ async function linkPackage(packageDir, options, addToConfig, keyword) { results = await execa(`yarn`, ['link', packageName]); console.log(results.stdout); + // Add the node_modules of the linked package so that webpack + // can find the linked package externals if there are + const webpackPwaPath = path.join( + viewerDirectory, + '.webpack', + 'webpack.pwa.js' + ); + + async function updateWebpackConfig(webpackConfigPath, packageDir) { + const packageNodeModules = path.join(packageDir, 'node_modules'); + const fileContent = await fs.promises.readFile(webpackConfigPath, 'utf8'); + + const newLine = `path.resolve(__dirname, '${packageNodeModules}'),`; + const modifiedFileContent = fileContent.replace( + /(modules:\s*\[)([\s\S]*?)(\])/, + `$1$2 ${newLine}$3` + ); + + await fs.promises.writeFile(webpackConfigPath, modifiedFileContent); + } + + await updateWebpackConfig(webpackPwaPath, packageDir); + // change directory to viewer packages and add the config item process.chdir(viewerDirectory); - addToConfig(packageName, { version }); + addToConfig(packageName, { + version, + }); + + // run prettier on the webpack config + results = await execa(`yarn`, ['prettier', '--write', webpackPwaPath]); } function linkExtension(packageDir, options) { diff --git a/platform/cli/src/commands/unlinkPackage.js b/platform/cli/src/commands/unlinkPackage.js index e192714ba..463e74964 100644 --- a/platform/cli/src/commands/unlinkPackage.js +++ b/platform/cli/src/commands/unlinkPackage.js @@ -1,4 +1,6 @@ import { execa } from 'execa'; +import fs from 'fs'; +import path from 'path'; import { validateYarn, removeExtensionFromConfig, @@ -17,10 +19,51 @@ const linkPackage = async (packageName, options, removeFromConfig) => { const results = await execa(`yarn`, ['unlink', packageName]); console.log(results.stdout); + const webpackPwaPath = path.join( + viewerDirectory, + '.webpack', + 'webpack.pwa.js' + ); + + await removePathFromWebpackConfig(webpackPwaPath, packageName); + //update the plugin.json file removeFromConfig(packageName); + + // run prettier on the webpack config + await execa(`yarn`, ['prettier', '--write', webpackPwaPath]); }; +async function removePathFromWebpackConfig(webpackConfigPath, packageName) { + const fileContent = await fs.promises.readFile(webpackConfigPath, 'utf8'); + + const packageNameSubstring = `${packageName}/node_modules`; + const pathResolveStart = 'path.resolve('; + const closingParenthesis = ')'; + + let startIndex = fileContent.indexOf(packageNameSubstring); + + if (startIndex === -1) { + return; + } + + // Find the start of the "path.resolve" line. + startIndex = fileContent.lastIndexOf(pathResolveStart, startIndex); + + // Find the end of the line with the closing parenthesis. + let endIndex = fileContent.indexOf(closingParenthesis, startIndex) + 1; + + // Check if there's a comma after the closing parenthesis and remove it as well. + if (fileContent[endIndex] === ',') { + endIndex++; + } + + const modifiedFileContent = + fileContent.slice(0, startIndex) + fileContent.slice(endIndex); + + await fs.promises.writeFile(webpackConfigPath, modifiedFileContent); +} + function unlinkExtension(extensionName, options) { linkPackage(extensionName, options, removeExtensionFromConfig); } diff --git a/platform/cli/src/commands/utils/private/writePluginConfigFile.js b/platform/cli/src/commands/utils/private/writePluginConfigFile.js index eaef52343..9ff9a4b7e 100644 --- a/platform/cli/src/commands/utils/private/writePluginConfigFile.js +++ b/platform/cli/src/commands/utils/private/writePluginConfigFile.js @@ -6,9 +6,9 @@ export default function writePluginConfigFile(pluginConfig) { fs.writeFileSync( `./pluginConfig.json`, - jsonStringOfFileContents, + jsonStringOfFileContents + '\n', // Add a newline character at the end { flag: 'w+' }, - (err) => { + err => { if (err) { console.error(err); return; diff --git a/platform/cli/src/questions.js b/platform/cli/src/questions.js index 1d976a353..26f207d7c 100644 --- a/platform/cli/src/questions.js +++ b/platform/cli/src/questions.js @@ -1,4 +1,5 @@ import path from 'path'; +import os from 'os'; function getPathQuestions(packageType) { return [ @@ -6,7 +7,7 @@ function getPathQuestions(packageType) { type: 'input', name: 'name', message: `What is the name of your ${packageType}?`, - validate: (input) => { + validate: input => { if (!input) { return 'Please enter a name'; } @@ -17,8 +18,8 @@ function getPathQuestions(packageType) { { type: 'input', name: 'baseDir', - message: `What is the target absolute path to create your ${packageType} (we recommend you do not use the OHIF ${packageType} folder (./${packageType}s) unless you are developing a core ${packageType}):`, - validate: (input) => { + message: `What is the target path to create your ${packageType} (we recommend you do not use the OHIF ${packageType} folder (./${packageType}s) unless you are developing a core ${packageType}):`, + validate: input => { if (!input) { console.log('Please provide a valid target directory path'); return; @@ -26,7 +27,13 @@ function getPathQuestions(packageType) { return true; }, filter: (input, answers) => { - return path.resolve(input, answers.name); + // Replace ~ with the user's home directory + const expandedPath = input.replace(/^~(?=$|\/|\\)/, os.homedir()); + + // Resolve the path to an absolute path + const resolvedPath = path.resolve(expandedPath, answers.name); + + return resolvedPath; }, }, { @@ -43,6 +50,7 @@ function getRepoQuestions(packageType) { type: 'confirm', name: 'gitRepository', message: 'Should it be a git repository?', + default: false, }, { type: 'confirm', diff --git a/platform/cli/templates/mode/src/index.tsx b/platform/cli/templates/mode/src/index.tsx index a9c28dd93..2086aa36b 100644 --- a/platform/cli/templates/mode/src/index.tsx +++ b/platform/cli/templates/mode/src/index.tsx @@ -1,4 +1,6 @@ +import { hotkeys } from '@ohif/core'; import { id } from './id'; +import { initToolGroups, toolbarButtons } from '@ohif/mode-longitudinal'; const ohif = { layout: '@ohif/extension-default.layoutTemplateModule.viewerLayout', @@ -38,12 +40,76 @@ function modeFactory({ modeConfiguration }) { * Runs when the Mode Route is mounted to the DOM. Usually used to initialize * Services and other resources. */ - onModeEnter: ({ servicesManager, extensionManager }) => {}, - /** - * Runs when the Mode Route is unmounted from the DOM. Usually used to clean - * up resources and states - */ - onModeExit: () => {}, + onModeEnter: ({ servicesManager, extensionManager, commandsManager }) => { + const { + measurementService, + toolbarService, + toolGroupService, + } = servicesManager.services; + + measurementService.clearMeasurements(); + + // Init Default and SR ToolGroups + initToolGroups(extensionManager, toolGroupService, commandsManager); + + let unsubscribe; + + const activateTool = () => { + toolbarService.recordInteraction({ + groupId: 'WindowLevel', + itemId: 'WindowLevel', + interactionType: 'tool', + commands: [ + { + commandName: 'setToolActive', + commandOptions: { + toolName: 'WindowLevel', + }, + context: 'CORNERSTONE', + }, + ], + }); + + // We don't need to reset the active tool whenever a viewport is getting + // added to the toolGroup. + unsubscribe(); + }; + + // Since we only have one viewport for the basic cs3d mode and it has + // only one hanging protocol, we can just use the first viewport + ({ unsubscribe } = toolGroupService.subscribe( + toolGroupService.EVENTS.VIEWPORT_ADDED, + activateTool + )); + + toolbarService.init(extensionManager); + toolbarService.addButtons(toolbarButtons); + toolbarService.createButtonSection('primary', [ + 'MeasurementTools', + 'Zoom', + 'WindowLevel', + 'Pan', + 'Capture', + 'Layout', + 'MPR', + 'Crosshairs', + 'MoreTools', + ]); + }, + onModeExit: ({ servicesManager }) => { + const { + toolGroupService, + syncGroupService, + toolbarService, + segmentationService, + cornerstoneViewportService, + } = servicesManager.services; + + toolGroupService.destroy(); + syncGroupService.destroy(); + segmentationService.destroy(); + cornerstoneViewportService.destroy(); + }, /** */ validationTags: { study: [], @@ -93,7 +159,7 @@ function modeFactory({ modeConfiguration }) { /** SopClassHandlers used by the mode */ sopClassHandlers: [ohif.sopClassHandler], /** hotkeys for mode */ - hotkeys: [''], + hotkeys: [...hotkeys.defaults.hotkeyBindings], }; } diff --git a/platform/docs/docs/development/ohif-cli.md b/platform/docs/docs/development/ohif-cli.md index dc3f95069..ad55b071c 100644 --- a/platform/docs/docs/development/ohif-cli.md +++ b/platform/docs/docs/development/ohif-cli.md @@ -292,7 +292,7 @@ are currently being used by the viewer. ## Private NPM Repos -For the `yarn cli` to view private NPM repos, create a read-only token with the +For the `yarn cli` to view private NPM repos, create a read-only token with the following steps and export it as an environmental variable. You may also export an existing npm token. ``` @@ -300,3 +300,9 @@ npm login npm token create --read-only export NPM_TOKEN= ``` + +## External dependencies +The ohif-cli will add the path to the external dependencies to the webpack config, +so that you can install them in your project and use them in your custom +extensions and modes. To achieve this ohif-cli will update the webpack.pwa.js +file in the platform/viewer directory. diff --git a/platform/docs/versioned_docs/version-3.0/platform/themeing.md b/platform/docs/versioned_docs/version-3.0/platform/themeing.md index 48a881c20..852c5d398 100644 --- a/platform/docs/versioned_docs/version-3.0/platform/themeing.md +++ b/platform/docs/versioned_docs/version-3.0/platform/themeing.md @@ -127,7 +127,9 @@ window.config = { > You can simply use the stylings from tailwind CSS in the whiteLabeling -In addition to text, you can also add your custom logo +In addition to text, you can also add your custom logo. You can put them +inside the platform/viewer/public/assets folder and use them in the +whiteLabeling section. ```js window.config = { @@ -143,7 +145,7 @@ window.config = { href: '/', }, React.createElement('img', { - src: './customLogo.svg', + src: './assets/customLogo.svg', // className: 'w-8 h-8', }) ); diff --git a/platform/ui/src/components/Thumbnail/Thumbnail.tsx b/platform/ui/src/components/Thumbnail/Thumbnail.tsx index 23b080c20..dad5b6ea1 100644 --- a/platform/ui/src/components/Thumbnail/Thumbnail.tsx +++ b/platform/ui/src/components/Thumbnail/Thumbnail.tsx @@ -52,7 +52,7 @@ const Thumbnail = ({ 'flex flex-1 items-center justify-center rounded-md bg-black text-base text-white overflow-hidden min-h-32', isActive ? 'border-2 border-primary-light' - : 'border border-secondary-light group-focus:border-blue-300 hover:border-blue-300' + : 'border border-secondary-light hover:border-blue-300' )} style={{ margin: isActive ? '0' : '1px', diff --git a/platform/viewer/.webpack/webpack.pwa.js b/platform/viewer/.webpack/webpack.pwa.js index 43b073a71..0da6104f5 100644 --- a/platform/viewer/.webpack/webpack.pwa.js +++ b/platform/viewer/.webpack/webpack.pwa.js @@ -106,7 +106,7 @@ module.exports = (env, argv) => { '../../../node_modules/dicom-microscopy-viewer/dist/dynamic-import', to: DIST_DIR, globOptions: { - ignore: ['*.js.map'], + ignore: ['**/*.min.js.map'], }, }, // Copy dicom-image-loader build files diff --git a/platform/viewer/public/config/aws.js b/platform/viewer/public/config/aws.js index b6a2649cc..35ffbde5c 100644 --- a/platform/viewer/public/config/aws.js +++ b/platform/viewer/public/config/aws.js @@ -1,6 +1,5 @@ window.config = { routerBasename: '/', - // whiteLabelling: {}, extensions: [], modes: [], showStudyList: true, @@ -11,6 +10,7 @@ window.config = { showLoadingIndicator: true, strictZSpacingForVolumeViewport: true, // filterQueryParam: false, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'dcmjs DICOMWeb Server', @@ -54,26 +54,6 @@ window.config = { // Could use services manager here to bring up a dialog/modal if needed. console.warn('test, navigate to https://ohif.org/'); }, - // whiteLabeling: { - // /* Optional: Should return a React component to be rendered in the "Logo" section of the application's Top Navigation bar */ - // createLogoComponentFn: function (React) { - // return React.createElement( - // 'a', - // { - // target: '_self', - // rel: 'noopener noreferrer', - // className: 'text-purple-600 line-through', - // href: '/', - // }, - // React.createElement('img', - // { - // src: './customLogo.svg', - // className: 'w-8 h-8', - // } - // )) - // }, - // }, - defaultDataSourceName: 'dicomweb', hotkeys: [ { commandName: 'incrementActiveViewport', diff --git a/platform/viewer/public/config/default.js b/platform/viewer/public/config/default.js index 05a408969..757bdc344 100644 --- a/platform/viewer/public/config/default.js +++ b/platform/viewer/public/config/default.js @@ -24,6 +24,7 @@ window.config = { prefetch: 25, }, // filterQueryParam: false, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'dcmjs DICOMWeb Server', @@ -96,13 +97,12 @@ window.config = { // }, // React.createElement('img', // { - // src: './customLogo.svg', + // src: './assets/customLogo.svg', // className: 'w-8 h-8', // } // )) // }, // }, - defaultDataSourceName: 'dicomweb', hotkeys: [ { commandName: 'incrementActiveViewport', diff --git a/platform/viewer/public/config/demo.js b/platform/viewer/public/config/demo.js index c9e17261d..59f01cc9c 100644 --- a/platform/viewer/public/config/demo.js +++ b/platform/viewer/public/config/demo.js @@ -8,6 +8,7 @@ window.config = { showWarningMessageForCrossOrigin: true, strictZSpacingForVolumeViewport: true, showCPUFallbackMessage: true, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'DCM4CHEE Server', @@ -25,7 +26,6 @@ window.config = { }, }, ], - defaultDataSourceName: 'dicomweb', hotkeys: [ { commandName: 'incrementActiveViewport', diff --git a/platform/viewer/public/config/dicomweb-server.js b/platform/viewer/public/config/dicomweb-server.js index 770d94af3..4db990417 100644 --- a/platform/viewer/public/config/dicomweb-server.js +++ b/platform/viewer/public/config/dicomweb-server.js @@ -1,6 +1,5 @@ window.config = { routerBasename: '/', - // whiteLabelling: {}, extensions: [], modes: [], showStudyList: true, @@ -11,6 +10,7 @@ window.config = { showLoadingIndicator: true, strictZSpacingForVolumeViewport: true, // filterQueryParam: false, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'dcmjs DICOMWeb Server', @@ -45,5 +45,4 @@ window.config = { configuration: {}, }, ], - defaultDataSourceName: 'dicomweb', }; diff --git a/platform/viewer/public/config/dicomweb_relative.js b/platform/viewer/public/config/dicomweb_relative.js index 1e0111975..af024abd7 100644 --- a/platform/viewer/public/config/dicomweb_relative.js +++ b/platform/viewer/public/config/dicomweb_relative.js @@ -1,6 +1,5 @@ window.config = { routerBasename: '/', - // whiteLabelling: {}, extensions: [], modes: [], showStudyList: true, @@ -12,6 +11,7 @@ window.config = { showLoadingIndicator: true, strictZSpacingForVolumeViewport: true, // filterQueryParam: false, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'Static WADO Local Data', @@ -55,26 +55,6 @@ window.config = { // Could use services manager here to bring up a dialog/modal if needed. console.warn('test, navigate to https://ohif.org/'); }, - // whiteLabeling: { - // /* Optional: Should return a React component to be rendered in the "Logo" section of the application's Top Navigation bar */ - // createLogoComponentFn: function (React) { - // return React.createElement( - // 'a', - // { - // target: '_self', - // rel: 'noopener noreferrer', - // className: 'text-purple-600 line-through', - // href: '/', - // }, - // React.createElement('img', - // { - // src: './customLogo.svg', - // className: 'w-8 h-8', - // } - // )) - // }, - // }, - defaultDataSourceName: 'dicomweb', hotkeys: [ { commandName: 'incrementActiveViewport', diff --git a/platform/viewer/public/config/docker_nginx-orthanc.js b/platform/viewer/public/config/docker_nginx-orthanc.js index d33fcfcb0..60d7f083c 100644 --- a/platform/viewer/public/config/docker_nginx-orthanc.js +++ b/platform/viewer/public/config/docker_nginx-orthanc.js @@ -9,6 +9,7 @@ window.config = { showCPUFallbackMessage: true, showLoadingIndicator: true, strictZSpacingForVolumeViewport: true, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'Orthanc Server', @@ -39,5 +40,4 @@ window.config = { configuration: {}, }, ], - defaultDataSourceName: 'dicomweb', }; diff --git a/platform/viewer/public/config/docker_openresty-orthanc.js b/platform/viewer/public/config/docker_openresty-orthanc.js index 39cfebd68..33e413877 100644 --- a/platform/viewer/public/config/docker_openresty-orthanc.js +++ b/platform/viewer/public/config/docker_openresty-orthanc.js @@ -9,6 +9,7 @@ window.config = { showCPUFallbackMessage: true, showLoadingIndicator: true, strictZSpacingForVolumeViewport: true, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'Orthanc Server', @@ -39,5 +40,4 @@ window.config = { configuration: {}, }, ], - defaultDataSourceName: 'dicomweb', }; diff --git a/platform/viewer/public/config/e2e.js b/platform/viewer/public/config/e2e.js index 0decbb941..a2b9ff8b5 100644 --- a/platform/viewer/public/config/e2e.js +++ b/platform/viewer/public/config/e2e.js @@ -10,6 +10,7 @@ window.config = { showCPUFallbackMessage: false, strictZSpacingForVolumeViewport: true, // filterQueryParam: false, + defaultDataSourceName: 'e2e', dataSources: [ { friendlyName: 'StaticWado test data', @@ -118,25 +119,5 @@ window.config = { // Could use services manager here to bring up a dialog/modal if needed. console.warn('test, navigate to https://ohif.org/'); }, - // whiteLabeling: { - // /* Optional: Should return a React component to be rendered in the "Logo" section of the application's Top Navigation bar */ - // createLogoComponentFn: function (React) { - // return React.createElement( - // 'a', - // { - // target: '_self', - // rel: 'noopener noreferrer', - // className: 'text-purple-600 line-through', - // href: '/', - // }, - // React.createElement('img', - // { - // src: './customLogo.svg', - // className: 'w-8 h-8', - // } - // )) - // }, - // }, - defaultDataSourceName: 'e2e', hotkeys: [], }; diff --git a/platform/viewer/public/config/google.js b/platform/viewer/public/config/google.js index 768bd1bc9..847e08ebb 100644 --- a/platform/viewer/public/config/google.js +++ b/platform/viewer/public/config/google.js @@ -30,11 +30,11 @@ window.config = { revokeAccessTokenOnSignout: true, }, ], - // whiteLabelling: {}, extensions: [], modes: [], showStudyList: true, // filterQueryParam: false, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'dcmjs DICOMWeb Server', @@ -72,5 +72,4 @@ window.config = { configuration: {}, }, ], - defaultDataSourceName: 'dicomweb', }; diff --git a/platform/viewer/public/config/local_dcm4chee.js b/platform/viewer/public/config/local_dcm4chee.js index 44dbba9d3..d47c4c34a 100644 --- a/platform/viewer/public/config/local_dcm4chee.js +++ b/platform/viewer/public/config/local_dcm4chee.js @@ -13,6 +13,7 @@ window.config = { showCPUFallbackMessage: true, showLoadingIndicator: true, strictZSpacingForVolumeViewport: true, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'DCM4CHEE Server', @@ -49,5 +50,4 @@ window.config = { }, ], studyListFunctionsEnabled: true, - defaultDataSourceName: 'dicomweb', }; diff --git a/platform/viewer/public/config/local_orthanc.js b/platform/viewer/public/config/local_orthanc.js index 9b5d086b6..140f4d516 100644 --- a/platform/viewer/public/config/local_orthanc.js +++ b/platform/viewer/public/config/local_orthanc.js @@ -1,6 +1,5 @@ window.config = { routerBasename: '/', - // whiteLabelling: {}, extensions: [], modes: [], customizationService: { @@ -14,6 +13,7 @@ window.config = { showCPUFallbackMessage: true, strictZSpacingForVolumeViewport: true, // filterQueryParam: false, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'dcmjs DICOMWeb Server', @@ -57,26 +57,6 @@ window.config = { // Could use services manager here to bring up a dialog/modal if needed. console.warn('test, navigate to https://ohif.org/'); }, - // whiteLabeling: { - // /* Optional: Should return a React component to be rendered in the "Logo" section of the application's Top Navigation bar */ - // createLogoComponentFn: function (React) { - // return React.createElement( - // 'a', - // { - // target: '_self', - // rel: 'noopener noreferrer', - // className: 'text-purple-600 line-through', - // href: '/', - // }, - // React.createElement('img', - // { - // src: './customLogo.svg', - // className: 'w-8 h-8', - // } - // )) - // }, - // }, - defaultDataSourceName: 'dicomweb', hotkeys: [ { commandName: 'incrementActiveViewport', diff --git a/platform/viewer/public/config/local_static.js b/platform/viewer/public/config/local_static.js index fde3c563c..6774e1b9a 100644 --- a/platform/viewer/public/config/local_static.js +++ b/platform/viewer/public/config/local_static.js @@ -14,6 +14,7 @@ window.config = { showLoadingIndicator: true, strictZSpacingForVolumeViewport: true, // filterQueryParam: false, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'Static WADO Local Data', @@ -56,7 +57,6 @@ window.config = { // Could use services manager here to bring up a dialog/modal if needed. console.warn('test, navigate to https://ohif.org/'); }, - defaultDataSourceName: 'dicomweb', hotkeys: [ { commandName: 'incrementActiveViewport', diff --git a/platform/viewer/public/config/multiple.js b/platform/viewer/public/config/multiple.js index 2aa6252dd..a5de22d0d 100644 --- a/platform/viewer/public/config/multiple.js +++ b/platform/viewer/public/config/multiple.js @@ -22,6 +22,7 @@ window.config = { showLoadingIndicator: true, strictZSpacingForVolumeViewport: true, // filterQueryParam: false, + defaultDataSourceName: 'default', dataSources: [ { friendlyName: 'Static WADO Local Data', @@ -131,7 +132,6 @@ window.config = { // Could use services manager here to bring up a dialog/modal if needed. console.warn('test, navigate to https://ohif.org/'); }, - defaultDataSourceName: 'default', // Only list the unique hotkeys hotkeys: [], diff --git a/platform/viewer/public/config/netlify.js b/platform/viewer/public/config/netlify.js index 405c276e5..c2187aca6 100644 --- a/platform/viewer/public/config/netlify.js +++ b/platform/viewer/public/config/netlify.js @@ -1,6 +1,5 @@ window.config = { routerBasename: '/', - // whiteLabelling: {}, extensions: [], modes: [], showStudyList: true, @@ -11,6 +10,7 @@ window.config = { showLoadingIndicator: true, strictZSpacingForVolumeViewport: true, // filterQueryParam: false, + defaultDataSourceName: 'dicomweb', dataSources: [ { friendlyName: 'dcmjs DICOMWeb Server', @@ -54,26 +54,6 @@ window.config = { // Could use services manager here to bring up a dialog/modal if needed. console.warn('test, navigate to https://ohif.org/'); }, - // whiteLabeling: { - // /* Optional: Should return a React component to be rendered in the "Logo" section of the application's Top Navigation bar */ - // createLogoComponentFn: function (React) { - // return React.createElement( - // 'a', - // { - // target: '_self', - // rel: 'noopener noreferrer', - // className: 'text-purple-600 line-through', - // href: '/', - // }, - // React.createElement('img', - // { - // src: './customLogo.svg', - // className: 'w-8 h-8', - // } - // )) - // }, - // }, - defaultDataSourceName: 'dicomweb', hotkeys: [ { commandName: 'incrementActiveViewport', From a688f03fdb3dd8e56e31b3b298392e52e384d5fc Mon Sep 17 00:00:00 2001 From: Bill Wallace Date: Mon, 8 May 2023 21:18:35 -0400 Subject: [PATCH 33/54] feat(App): Loads mode extensions on demand (#3312) * feat: Dynamic plugin imports * Remove unused file * Fix basic dev mode * Fix the modes issue that Joe requested * Merge fixes * Add the ability to publish directory contents * PR review changes --------- --- modes/basic-dev-mode/src/index.js | 16 ++- platform/public/demo.html | 9 ++ .../viewer/.webpack/writePluginImportsFile.js | 101 +++++++++--------- platform/viewer/pluginConfig.json | 79 +++++++++----- platform/viewer/public/config/multiple.js | 2 +- platform/viewer/src/appInit.js | 50 ++++++--- platform/viewer/src/index.js | 35 +++--- platform/viewer/src/routes/Mode/Mode.tsx | 86 ++++++++------- .../viewer/src/routes/WorkList/WorkList.tsx | 2 +- .../viewer/src/routes/buildModeRoutes.tsx | 3 - .../src/routes/checkExtensionDependencies.js | 39 ------- 11 files changed, 225 insertions(+), 197 deletions(-) create mode 100644 platform/public/demo.html delete mode 100644 platform/viewer/src/routes/checkExtensionDependencies.js diff --git a/modes/basic-dev-mode/src/index.js b/modes/basic-dev-mode/src/index.js index 875d26212..0f769854e 100644 --- a/modes/basic-dev-mode/src/index.js +++ b/modes/basic-dev-mode/src/index.js @@ -10,7 +10,6 @@ const configs = { const ohif = { layout: '@ohif/extension-default.layoutTemplateModule.viewerLayout', sopClassHandler: '@ohif/extension-default.sopClassHandlerModule.stack', - hangingProtocol: '@ohif/extension-default.hangingProtocolModule.default', measurements: '@ohif/extension-default.panelModule.measure', thumbnailList: '@ohif/extension-default.panelModule.seriesList', }; @@ -47,8 +46,8 @@ const extensionDependencies = { function modeFactory({ modeConfiguration }) { return { id, - routeName: 'viewer', - displayName: 'Basic Viewer CS3D', + routeName: 'dev', + displayName: 'Basic Dev Viewer', /** * Lifecycle hooks */ @@ -134,6 +133,15 @@ function modeFactory({ modeConfiguration }) { 'MoreTools', ]); }, + onModeExit: ({ servicesManager }) => { + const { + toolGroupService, + measurementService, + toolbarService, + } = servicesManager.services; + + toolGroupService.destroy(); + }, validationTags: { study: [], series: [], @@ -177,7 +185,7 @@ function modeFactory({ modeConfiguration }) { }, ], extensions: extensionDependencies, - hangingProtocol: [ohif.hangingProtocol], + hangingProtocol: 'default', sopClassHandlers: [ dicomvideo.sopClassHandler, ohif.sopClassHandler, diff --git a/platform/public/demo.html b/platform/public/demo.html new file mode 100644 index 000000000..7b3a647ed --- /dev/null +++ b/platform/public/demo.html @@ -0,0 +1,9 @@ + + +

Demo Page

+

This demo page shows how to include directories of content in the pluginConfig.json file. + The idea is that it is possible to serve up non-compiled content such as the microscopy mode + which will not be included in the compile of OHIF but can be included later on dynamically. +

+ + diff --git a/platform/viewer/.webpack/writePluginImportsFile.js b/platform/viewer/.webpack/writePluginImportsFile.js index d3d2667fd..41caf84b6 100644 --- a/platform/viewer/.webpack/writePluginImportsFile.js +++ b/platform/viewer/.webpack/writePluginImportsFile.js @@ -1,11 +1,14 @@ const pluginConfig = require('../pluginConfig.json'); const fs = require('fs'); +const os = require('os'); const glob = require('glob'); const autogenerationDisclaimer = ` // THIS FILE IS AUTOGENERATED AS PART OF THE EXTENSION AND MODE PLUGIN PROCESS. // IT SHOULD NOT BE MODIFIED MANUALLY \n`; +const extractName = (val) => (typeof val === 'string') ? val : val.packageName; + function constructLines(input, categoryName) { let pluginCount = 0; @@ -19,14 +22,10 @@ function constructLines(input, categoryName) { input.forEach(entry => { if (entry.default === false) return; - const packageName = entry.packageName; - const defaultImportName = `${categoryName}${pluginCount}`; + const packageName = extractName(entry); - lines.importLines.push( - `import ${defaultImportName} from '${packageName}';\n` - ); lines.addToWindowLines.push( - `${categoryName}.push(${defaultImportName});\n` + `${categoryName}.push("${packageName}");\n` ); pluginCount++; @@ -49,7 +48,7 @@ function getFormattedWindowBlock(addToWindowLines) { let content = 'const extensions = [];\n' + 'const modes = [];\n' + - 'const modesFactory = [];\n' + + '\n// Not required any longer\n' + 'window.extensions = extensions;\n' + 'window.modes = modes;\n\n'; @@ -60,47 +59,55 @@ function getFormattedWindowBlock(addToWindowLines) { return content; } -function getRuntimeLoadModesExtensions() { - return ( - '\n\n// Add a dynamic runtime loader\n' + - 'export default async () => {\n' + - ' for(const modeFactory of modesFactory) {\n' + - ' const newModes = await modeFactory(modes,extensions);\n' + - ' newModes.forEach(newMode => modes.push(newMode));\n' + - '}\n}\n\n\n' + - 'async function loadRuntimeImports(config) {\n' + - ' if (config && config.modes && config.modes.length) {\n' + - ' for (const modeName of config.modes) {\n' + - ' const existingMode = modes.find(mode => mode.id === modeName);\n' + - ' if (!existingMode) {\n' + - ' if (modeName === `@ohif/mode-test`) {\n' + - ' const mode = await import(`@ohif/mode-test`);\n' + - ' window.modes.push(mode.default);\n' + - ' const extension = await import(`@ohif/extension-test`);\n' + - ' window.extensions.push(extension.default);\n' + - ' }\n' + - ' }\n' + - ' };\n' + - ' }\n' + - '}\n' + - 'export { loadRuntimeImports };\n\n' - ); +function getRuntimeLoadModesExtensions(modules) { + const dynamicLoad = []; + dynamicLoad.push( + '\n\n// Add a dynamic runtime loader', + 'async function loadModule(module) {', + ' if (typeof module !== \'string\') return module;'); + modules.forEach(module => { + const packageName = extractName(module); + dynamicLoad.push( + ` if( module==="${packageName}") {`, + ` const imported = await import("${packageName}");`, + ' return imported.default;', + ' }' + ); + }) + dynamicLoad.push( + ' return (await import(module)).default;', + '}\n', + '// Import a list of items (modules or string names)', + '// @return a Promise evaluating to a list of modules', + 'export default function importItems(modules) {', + ' return Promise.all(modules.map(loadModule));', + '}\n', + 'export { loadModule, modes, extensions, importItems };\n\n'); + return dynamicLoad.join('\n'); +} + +const fromDirectory = (srcDir, path) => { + if (!path) return; + if (path[0] === '.') return srcDir + '/../../..' + path.substring(1); + if (path[0] === '~') return os.homedir() + path.substring(1); + return path; } const createCopyPluginToDistForLink = ( - SRC_DIR, - DIST_DIR, + srcDir, + distDir, plugins, folderName ) => { return plugins .map(plugin => { - const from = `${SRC_DIR}/../node_modules/${plugin.packageName}/${folderName}/`; + const fromDir = fromDirectory(srcDir, plugin.directory); + const from = fromDir || `${srcDir}/../node_modules/${plugin.packageName}/${folderName}/`; const exists = fs.existsSync(from); return exists ? { from, - to: DIST_DIR, + to: distDir, toType: 'dir', } : undefined; @@ -134,23 +141,20 @@ function writePluginImportsFile(SRC_DIR, DIST_DIR) { const extensionLines = constructLines(pluginConfig.extensions, 'extensions'); const modeLines = constructLines(pluginConfig.modes, 'modes'); - const modesFactoryLines = constructLines( - pluginConfig.modesFactory, - 'modesFactory' - ); pluginImportsJsContent += getFormattedImportBlock([ ...extensionLines.importLines, ...modeLines.importLines, - ...modesFactoryLines.importLines, ]); pluginImportsJsContent += getFormattedWindowBlock([ ...extensionLines.addToWindowLines, ...modeLines.addToWindowLines, - ...modesFactoryLines.addToWindowLines, ]); - pluginImportsJsContent += getRuntimeLoadModesExtensions(); + pluginImportsJsContent += getRuntimeLoadModesExtensions([ + ...pluginConfig.extensions, + ...pluginConfig.modes, + ]); fs.writeFileSync( `${SRC_DIR}/pluginImports.js`, @@ -172,10 +176,8 @@ function writePluginImportsFile(SRC_DIR, DIST_DIR) { SRC_DIR, DIST_DIR, [ - ...pluginConfig.modesFactory, ...pluginConfig.modes, ...pluginConfig.extensions, - ...pluginConfig.umd, ], 'public' ); @@ -184,10 +186,9 @@ function writePluginImportsFile(SRC_DIR, DIST_DIR) { SRC_DIR, DIST_DIR, [ - ...pluginConfig.modesFactory, ...pluginConfig.modes, ...pluginConfig.extensions, - ...pluginConfig.umd, + ...pluginConfig.public, ], 'public' ); @@ -198,10 +199,8 @@ function writePluginImportsFile(SRC_DIR, DIST_DIR) { SRC_DIR, DIST_DIR, [ - ...pluginConfig.modesFactory, ...pluginConfig.modes, ...pluginConfig.extensions, - ...pluginConfig.umd, ], 'dist' ); @@ -210,15 +209,13 @@ function writePluginImportsFile(SRC_DIR, DIST_DIR) { SRC_DIR, DIST_DIR, [ - ...pluginConfig.modesFactory, ...pluginConfig.modes, ...pluginConfig.extensions, - ...pluginConfig.umd, ], 'dist' ); - console.log('copy plugins', [ + console.warn('copy plugins', [ ...copyPluginPublicToDistBuild, ...copyPluginPublicToDistLink, ...copyPluginDistToDistBuild, diff --git a/platform/viewer/pluginConfig.json b/platform/viewer/pluginConfig.json index 37e90e765..ec3743c95 100644 --- a/platform/viewer/pluginConfig.json +++ b/platform/viewer/pluginConfig.json @@ -1,60 +1,83 @@ { "extensions": [ + { + "packageName": "@ohif/extension-default" + }, { "packageName": "@ohif/extension-cornerstone", + "default": false, "version": "3.0.0" }, { "packageName": "@ohif/extension-measurement-tracking", + "default": false, "version": "3.0.0" }, { "packageName": "@ohif/extension-cornerstone-dicom-sr", - "version": "3.0.0" - }, - { - "packageName": "@ohif/extension-default", - "version": "3.0.0" - }, - { - "packageName": "@ohif/extension-dicom-microscopy", - "version": "3.0.0" - }, - { - "packageName": "@ohif/extension-dicom-pdf", - "version": "3.0.1" - }, - { - "packageName": "@ohif/extension-dicom-video", - "version": "3.0.1" - }, - { - "packageName": "@ohif/extension-tmtv", + "default": false, "version": "3.0.0" }, { "packageName": "@ohif/extension-cornerstone-dicom-seg", + "default": false, + "version": "3.0.0" + }, + { + "packageName": "@ohif/extension-dicom-microscopy", + "default": false, + "version": "3.0.0" + }, + { + "packageName": "@ohif/extension-dicom-pdf", + "default": false, + "version": "3.0.0" + }, + { + "packageName": "@ohif/extension-dicom-video", + "default": false, + "version": "3.0.0" + }, + { + "packageName": "@ohif/extension-tmtv", + "default": false, + "version": "3.0.0" + }, + { + "packageName": "@ohif/extension-test", + "default": false, "version": "3.0.0" }, { "packageName": "@ohif/extension-cornerstone-dicom-rt", + "default": false, "version": "3.0.0" } ], "modes": [ { - "packageName": "@ohif/mode-longitudinal", + "packageName": "@ohif/mode-longitudinal" + }, + { + "packageName": "@ohif/mode-tmtv" + }, + { + "packageName": "@ohif/mode-microscopy" + }, + { + "packageName": "@ohif/mode-test", + "default": false, "version": "3.0.0" }, { - "packageName": "@ohif/mode-microscopy", - "version": "3.0.0" - }, - { - "packageName": "@ohif/mode-tmtv", + "packageName": "@ohif/mode-basic-dev-mode", + "default": false, "version": "3.0.0" } ], - "modesFactory": [], - "umd": [] + "public": [ + { + "directory": "./platform/public" + } + ] } diff --git a/platform/viewer/public/config/multiple.js b/platform/viewer/public/config/multiple.js index a5de22d0d..d0e726caf 100644 --- a/platform/viewer/public/config/multiple.js +++ b/platform/viewer/public/config/multiple.js @@ -12,7 +12,7 @@ window.config = { }, ], extensions: [], - modes: ['@ohif/mode-test'], + modes: ['@ohif/mode-test', '@ohif/mode-basic-dev-mode'], showStudyList: true, maxNumberOfWebWorkers: 4, // below flag is for performance reasons, but it might not work for all servers diff --git a/platform/viewer/src/appInit.js b/platform/viewer/src/appInit.js index 58908c374..c6ddbf7ac 100644 --- a/platform/viewer/src/appInit.js +++ b/platform/viewer/src/appInit.js @@ -21,6 +21,8 @@ import { // utils, } from '@ohif/core'; +import loadModules from './pluginImports'; + /** * @param {object|func} appConfigOrFunc - application configuration, or a function that returns application configuration * @param {object[]} defaultExtensions - array of extension objects @@ -74,8 +76,12 @@ async function appInit(appConfigOrFunc, defaultExtensions, defaultModes) { * Example: [ext1, ext2, ext3] * Example2: [[ext1, config], ext2, [ext3, config]] */ + const loadedExtensions = await loadModules([ + ...defaultExtensions, + ...appConfig.extensions, + ]); await extensionManager.registerExtensions( - [...defaultExtensions, ...appConfig.extensions], + loadedExtensions, appConfig.dataSources ); @@ -87,24 +93,38 @@ async function appInit(appConfigOrFunc, defaultExtensions, defaultModes) { throw new Error('No modes are defined! Check your app-config.js'); } - for (let i = 0; i < defaultModes.length; i++) { - const { modeFactory, id } = defaultModes[i]; + const loadedModes = await loadModules([ + ...(appConfig.modes || []), + ...defaultModes, + ]); - // If the appConfig contains configuration for this mode, use it. - const modeConfig = - appConfig.modeConfig && appConfig.modeConfig[i] - ? appConfig.modeConfig[id] - : {}; + // This is the name for the loaded istance object + appConfig.loadedModes = []; + const modesById = new Set(); + for (let i = 0; i < loadedModes.length; i++) { + let mode = loadedModes[i]; + if (!mode) continue; + const { id } = mode; - const mode = modeFactory(modeConfig); + if (mode.modeFactory) { + // If the appConfig contains configuration for this mode, use it. + const modeConfig = + appConfig.modeConfig && appConfig.modeConfig[i] + ? appConfig.modeConfig[id] + : {}; - appConfig.modes.push(mode); + mode = mode.modeFactory(modeConfig); + } + + if (modesById.has(id)) continue; + // Prevent duplication + modesById.add(id); + if (!mode || typeof mode !== 'object') continue; + appConfig.loadedModes.push(mode); } - - // remove modes that are not objects, or have no id - appConfig.modes = appConfig.modes.filter( - mode => typeof mode === 'object' && mode.id - ); + // Hack alert - don't touch the original modes definition, + // but there are still dependencies on having the appConfig modes defined + appConfig.modes = appConfig.loadedModes; return { appConfig, diff --git a/platform/viewer/src/index.js b/platform/viewer/src/index.js index 6cec78ad2..71d48e2ef 100644 --- a/platform/viewer/src/index.js +++ b/platform/viewer/src/index.js @@ -16,25 +16,24 @@ import { history } from './utils/history'; * pluginImports.js imports all of the modes and extensions and adds them * to the window for processing. */ -import loadDynamicImports, { loadRuntimeImports } from './pluginImports.js'; +import { + modes as defaultModes, + extensions as defaultExtensions, +} from './pluginImports'; -loadDynamicImports().then(() => { - loadRuntimeImports(window.config).then(() => { - /** - * Combine our appConfiguration with installed extensions and modes. - * In the future appConfiguration may contain modes added at runtime. - * */ - const appProps = { - config: window ? window.config : {}, - defaultExtensions: window.extensions, - defaultModes: window.modes, - }; +/** + * Combine our appConfiguration with installed extensions and modes. + * In the future appConfiguration may contain modes added at runtime. + * */ +const appProps = { + config: window ? window.config : {}, + defaultExtensions, + defaultModes, +}; - /** Create App */ - const app = React.createElement(App, appProps, null); - /** Render */ - ReactDOM.render(app, document.getElementById('root')); - }); -}); +/** Create App */ +const app = React.createElement(App, appProps, null); +/** Render */ +ReactDOM.render(app, document.getElementById('root')); export { history }; diff --git a/platform/viewer/src/routes/Mode/Mode.tsx b/platform/viewer/src/routes/Mode/Mode.tsx index 7e7575bc0..9caf969a0 100644 --- a/platform/viewer/src/routes/Mode/Mode.tsx +++ b/platform/viewer/src/routes/Mode/Mode.tsx @@ -9,6 +9,7 @@ import ViewportGrid from '@components/ViewportGrid'; import Compose from './Compose'; import getStudies from './studiesList'; import { history } from '../../utils/history'; +import loadModules from '../../pluginImports'; const { getSplitParam } = utils; @@ -102,6 +103,8 @@ export default function ModeRoute({ const [studyInstanceUIDs, setStudyInstanceUIDs] = useState(); const [refresh, setRefresh] = useState(false); + const [allExtensionsLoaded, setAllExtensionsLoaded] = useState(false); + const layoutTemplateData = useRef(false); const locationRef = useRef(null); const isMounted = useRef(false); @@ -235,41 +238,52 @@ export default function ModeRoute({ return; } - // TODO: For some reason this is running before the Providers - // are calling setServiceImplementation - // TODO -> iterate through services. - - // Extension - - // Add SOPClassHandlers to a new SOPClassManager. - displaySetService.init(extensionManager, sopClassHandlers); - - extensionManager.onModeEnter({ - servicesManager, - extensionManager, - commandsManager, - }); - - // use the URL hangingProtocolId if it exists, otherwise use the one - // defined in the mode configuration - const hangingProtocolIdToUse = hangingProtocolService.getProtocolById( - runTimeHangingProtocolId - ) - ? runTimeHangingProtocolId - : hangingProtocol; - - // Sets the active hanging protocols - if hangingProtocol is undefined, - // resets to default. Done before the onModeEnter to allow the onModeEnter - // to perform custom hanging protocol actions - hangingProtocolService.setActiveProtocolIds(hangingProtocolIdToUse); - - mode?.onModeEnter({ - servicesManager, - extensionManager, - commandsManager, - }); - const setupRouteInit = async () => { + const loadedExtensions = await loadModules(Object.keys(extensions)); + for (const extension of loadedExtensions) { + const { id: extensionId } = extension; + if ( + extensionManager.registeredExtensionIds.indexOf(extensionId) === -1 + ) { + await extensionManager.registerExtension(extension); + } + } + setAllExtensionsLoaded(true); + + // TODO: For some reason this is running before the Providers + // are calling setServiceImplementation + // TODO -> iterate through services. + + // Extension + + // Add SOPClassHandlers to a new SOPClassManager. + displaySetService.init(extensionManager, sopClassHandlers); + + extensionManager.onModeEnter({ + servicesManager, + extensionManager, + commandsManager, + }); + + // use the URL hangingProtocolId if it exists, otherwise use the one + // defined in the mode configuration + const hangingProtocolIdToUse = hangingProtocolService.getProtocolById( + runTimeHangingProtocolId + ) + ? runTimeHangingProtocolId + : hangingProtocol; + + // Sets the active hanging protocols - if hangingProtocol is undefined, + // resets to default. Done before the onModeEnter to allow the onModeEnter + // to perform custom hanging protocol actions + hangingProtocolService.setActiveProtocolIds(hangingProtocolIdToUse); + + mode?.onModeEnter({ + servicesManager, + extensionManager, + commandsManager, + }); + /** * The next line should get all the query parameters provided by the URL * - except the StudyInstanceUIDs - and create an object called filters @@ -382,8 +396,8 @@ export default function ModeRoute({ {layoutTemplateData.current && - studyInstanceUIDs?.length && - studyInstanceUIDs[0] !== undefined && + studyInstanceUIDs?.[0] !== undefined && + allExtensionsLoaded && renderLayoutData({ ...layoutTemplateData.current.props, ViewportGridComp: ViewportGridWithDataSource, diff --git a/platform/viewer/src/routes/WorkList/WorkList.tsx b/platform/viewer/src/routes/WorkList/WorkList.tsx index 52d8928ca..f1987751c 100644 --- a/platform/viewer/src/routes/WorkList/WorkList.tsx +++ b/platform/viewer/src/routes/WorkList/WorkList.tsx @@ -336,7 +336,7 @@ function WorkList({ : [] } > - {appConfig.modes.map((mode, i) => { + {appConfig.loadedModes.map((mode, i) => { const isFirst = i === 0; const isValidMode = mode.isValidMode({ modalities }); diff --git a/platform/viewer/src/routes/buildModeRoutes.tsx b/platform/viewer/src/routes/buildModeRoutes.tsx index e87eb186e..c3375788d 100644 --- a/platform/viewer/src/routes/buildModeRoutes.tsx +++ b/platform/viewer/src/routes/buildModeRoutes.tsx @@ -1,6 +1,5 @@ import React from 'react'; import ModeRoute from '@routes/Mode'; -import checkExtensionDependencies from './checkExtensionDependencies'; /* Routes uniquely define an entry point to: @@ -41,8 +40,6 @@ export default function buildModeRoutes({ }); modes.forEach(mode => { - checkExtensionDependencies(mode, extensionManager); - // todo: for each route. add route to path. dataSourceNames.forEach(dataSourceName => { const path = `/${mode.routeName}/${dataSourceName}`; diff --git a/platform/viewer/src/routes/checkExtensionDependencies.js b/platform/viewer/src/routes/checkExtensionDependencies.js deleted file mode 100644 index 7fb8f61a7..000000000 --- a/platform/viewer/src/routes/checkExtensionDependencies.js +++ /dev/null @@ -1,39 +0,0 @@ -export default function checkExtensionDependencies(mode, extensionManager) { - const extensionDependencies = mode.extensions; - - const dependencyString = `Unmet extension dependency in mode: ${mode.id}`; - - Object.keys(extensionDependencies).forEach(extensionId => { - const extensionInstalled = extensionManager.registeredExtensionIds.includes( - extensionId - ); - - if (!extensionInstalled) { - throw new Error( - `${dependencyString}: extension ${extensionId} not found` - ); - } - }); -} - -function areVersionsCompatible(semanticVersion, installedVersion) { - if (semanticVersion.includes('^')) { - // Major must match - const versionLessCaret = semanticVersion.split('^')[1]; - - // Index 0 is the major version. - return versionLessCaret[0] === installedVersion[0]; - } else if (semanticVersion.includes('~')) { - // Major and minor must match - const versionLessTilde = semanticVersion.split('~')[1]; - - // Index 0 is the major version. - // Index 2 is the minor version. - return ( - versionLessTilde[0] === installedVersion[0] && - versionLessTilde[2] === installedVersion[2] - ); - } else { - return semanticVersion === installedVersion; - } -} From 98d966514a026bdb23c7167f21e96e03c198e6fd Mon Sep 17 00:00:00 2001 From: Joe Boccanfuso <109477394+jbocce@users.noreply.github.com> Date: Tue, 9 May 2023 12:15:26 -0400 Subject: [PATCH 34/54] fix(Measurements): edit measurement while SEG loaded (#3375) --- extensions/cornerstone/src/services/ViewportService/Viewport.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/extensions/cornerstone/src/services/ViewportService/Viewport.ts b/extensions/cornerstone/src/services/ViewportService/Viewport.ts index a99fa56af..e5b36342f 100644 --- a/extensions/cornerstone/src/services/ViewportService/Viewport.ts +++ b/extensions/cornerstone/src/services/ViewportService/Viewport.ts @@ -126,7 +126,7 @@ class ViewportInfo { if (!this.viewportData?.data) return false; if (this.viewportData.data.length) { - return !!this.viewportData.find(data => + return !!this.viewportData.data.find(data => dataContains(data, displaySetUID, imageId) ); } From 0b4c3649e748d3a78857c405e2cd0a666d02594c Mon Sep 17 00:00:00 2001 From: Alireza Date: Tue, 9 May 2023 12:26:16 -0400 Subject: [PATCH 35/54] fix(dynamic load): make sure required extensions are loaded (#3377) * fixes some bugs * make cornerstone default for now --- platform/viewer/pluginConfig.json | 1 - platform/viewer/src/routes/Mode/Mode.tsx | 54 ++++++++++++++++-------- 2 files changed, 36 insertions(+), 19 deletions(-) diff --git a/platform/viewer/pluginConfig.json b/platform/viewer/pluginConfig.json index ec3743c95..2f892db6c 100644 --- a/platform/viewer/pluginConfig.json +++ b/platform/viewer/pluginConfig.json @@ -5,7 +5,6 @@ }, { "packageName": "@ohif/extension-cornerstone", - "default": false, "version": "3.0.0" }, { diff --git a/platform/viewer/src/routes/Mode/Mode.tsx b/platform/viewer/src/routes/Mode/Mode.tsx index 9caf969a0..81badddff 100644 --- a/platform/viewer/src/routes/Mode/Mode.tsx +++ b/platform/viewer/src/routes/Mode/Mode.tsx @@ -103,7 +103,10 @@ export default function ModeRoute({ const [studyInstanceUIDs, setStudyInstanceUIDs] = useState(); const [refresh, setRefresh] = useState(false); - const [allExtensionsLoaded, setAllExtensionsLoaded] = useState(false); + const [ + ExtensionDependenciesLoaded, + setExtensionDependenciesLoaded, + ] = useState(false); const layoutTemplateData = useRef(false); const locationRef = useRef(null); @@ -169,6 +172,23 @@ export default function ModeRoute({ return ViewportGrid({ ...props, dataSource }); } + useEffect(() => { + const loadExtensions = async () => { + const loadedExtensions = await loadModules(Object.keys(extensions)); + for (const extension of loadedExtensions) { + const { id: extensionId } = extension; + if ( + extensionManager.registeredExtensionIds.indexOf(extensionId) === -1 + ) { + await extensionManager.registerExtension(extension); + } + } + setExtensionDependenciesLoaded(true); + }; + + loadExtensions(); + }, []); + useEffect(() => { // Preventing state update for unmounted component isMounted.current = true; @@ -178,6 +198,10 @@ export default function ModeRoute({ }, []); useEffect(() => { + if (!ExtensionDependenciesLoaded) { + return; + } + // Todo: this should not be here, data source should not care about params const initializeDataSource = async (params, query) => { const studyInstanceUIDs = await dataSource.initialize({ @@ -191,9 +215,13 @@ export default function ModeRoute({ return () => { layoutTemplateData.current = null; }; - }, [location]); + }, [location, ExtensionDependenciesLoaded]); useEffect(() => { + if (!ExtensionDependenciesLoaded) { + return; + } + const retrieveLayoutData = async () => { const layoutData = await route.layoutTemplate({ location, @@ -211,10 +239,10 @@ export default function ModeRoute({ return () => { layoutTemplateData.current = null; }; - }, [studyInstanceUIDs]); + }, [studyInstanceUIDs, ExtensionDependenciesLoaded]); useEffect(() => { - if (!hotkeys) { + if (!hotkeys || !ExtensionDependenciesLoaded) { return; } @@ -231,25 +259,14 @@ export default function ModeRoute({ return () => { hotkeysManager.destroy(); }; - }, []); + }, [ExtensionDependenciesLoaded]); useEffect(() => { - if (!layoutTemplateData.current) { + if (!layoutTemplateData.current || !ExtensionDependenciesLoaded) { return; } const setupRouteInit = async () => { - const loadedExtensions = await loadModules(Object.keys(extensions)); - for (const extension of loadedExtensions) { - const { id: extensionId } = extension; - if ( - extensionManager.registeredExtensionIds.indexOf(extensionId) === -1 - ) { - await extensionManager.registerExtension(extension); - } - } - setAllExtensionsLoaded(true); - // TODO: For some reason this is running before the Providers // are calling setServiceImplementation // TODO -> iterate through services. @@ -370,6 +387,7 @@ export default function ModeRoute({ mode, dataSourceName, location, + ExtensionDependenciesLoaded, route, servicesManager, extensionManager, @@ -397,7 +415,7 @@ export default function ModeRoute({ {layoutTemplateData.current && studyInstanceUIDs?.[0] !== undefined && - allExtensionsLoaded && + ExtensionDependenciesLoaded && renderLayoutData({ ...layoutTemplateData.current.props, ViewportGridComp: ViewportGridWithDataSource, From 55f996cf48a5578337d1fa01fccd5ea724a6769f Mon Sep 17 00:00:00 2001 From: Pavan Kumar Jadda <17564080+pavankjadda@users.noreply.github.com> Date: Tue, 9 May 2023 17:10:09 -0400 Subject: [PATCH 36/54] =?UTF-8?q?fix(service-worker):=20fixes=20service=20?= =?UTF-8?q?worker=20issue=20in=20init-service-worke=E2=80=A6=20(#3378)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- platform/viewer/public/init-service-worker.js | 85 ++++++++++--------- 1 file changed, 46 insertions(+), 39 deletions(-) diff --git a/platform/viewer/public/init-service-worker.js b/platform/viewer/public/init-service-worker.js index 22af800b5..0278c5747 100644 --- a/platform/viewer/public/init-service-worker.js +++ b/platform/viewer/public/init-service-worker.js @@ -3,50 +3,57 @@ // modules, so it's perfectly fine to serve this code to any browsers // (older browsers will just ignore it) // -import { Workbox } from 'https://storage.googleapis.com/workbox-cdn/releases/5.0.0-beta.1/workbox-window.prod.mjs'; +//import { Workbox } from './workbox-window.prod.mjs'; +// proper initialization +if( 'function' === typeof importScripts) { + importScripts( + 'https://storage.googleapis.com/workbox-cdn/releases/6.5.4/workbox-window.prod.mjs' + ); -var supportsServiceWorker = 'serviceWorker' in navigator; -var isNotLocalDevelopment = - ['localhost', '127'].indexOf(location.hostname) === -1; + var supportsServiceWorker = 'serviceWorker' in navigator; + var isNotLocalDevelopment = + ['localhost', '127'].indexOf(location.hostname) === -1; -if (supportsServiceWorker && isNotLocalDevelopment) { - const swFileLocation = (window.PUBLIC_URL || '/') + 'sw.js'; - const wb = new Workbox(swFileLocation); + if (supportsServiceWorker && isNotLocalDevelopment) { + const swFileLocation = (window.PUBLIC_URL || '/') + 'sw.js'; + const wb = new Workbox(swFileLocation); - // Add an event listener to detect when the registered - // service worker has installed but is waiting to activate. - wb.addEventListener('waiting', event => { - // customize the UI prompt accordingly. - const isFirstTimeUpdatedServiceWorkerIsWaiting = - event.wasWaitingBeforeRegister === false; - console.log( - 'isFirstTimeUpdatedServiceWorkerIsWaiting', - isFirstTimeUpdatedServiceWorkerIsWaiting - ); + // Add an event listener to detect when the registered + // service worker has installed but is waiting to activate. + wb.addEventListener('waiting', event => { + // customize the UI prompt accordingly. + const isFirstTimeUpdatedServiceWorkerIsWaiting = + event.wasWaitingBeforeRegister === false; + console.log( + 'isFirstTimeUpdatedServiceWorkerIsWaiting', + isFirstTimeUpdatedServiceWorkerIsWaiting + ); - // Assumes your app has some sort of prompt UI element - // that a user can either accept or reject. - // const prompt = createUIPrompt({ - // onAccept: async () => { - // Assuming the user accepted the update, set up a listener - // that will reload the page as soon as the previously waiting - // service worker has taken control. - wb.addEventListener('controlling', event => { - window.location.reload(); + // Assumes your app has some sort of prompt UI element + // that a user can either accept or reject. + // const prompt = createUIPrompt({ + // onAccept: async () => { + // Assuming the user accepted the update, set up a listener + // that will reload the page as soon as the previously waiting + // service worker has taken control. + wb.addEventListener('controlling', event => { + window.location.reload(); + }); + + // Send a message telling the service worker to skip waiting. + // This will trigger the `controlling` event handler above. + // Note: for this to work, you have to add a message + // listener in your service worker. See below. + wb.messageSW({ type: 'SKIP_WAITING' }); + // }, + + // onReject: () => { + // prompt.dismiss(); + // }, + // }); }); - // Send a message telling the service worker to skip waiting. - // This will trigger the `controlling` event handler above. - // Note: for this to work, you have to add a message - // listener in your service worker. See below. - wb.messageSW({ type: 'SKIP_WAITING' }); - // }, + wb.register(); + } - // onReject: () => { - // prompt.dismiss(); - // }, - // }); - }); - - wb.register(); } From 0eda151418c8894df63aac9be06919d3abed1d16 Mon Sep 17 00:00:00 2001 From: Joe Boccanfuso <109477394+jbocce@users.noreply.github.com> Date: Wed, 10 May 2023 09:07:17 -0400 Subject: [PATCH 37/54] fix(UI) - fixed the spacing and positioning of the close button in the SnackbarItem component (#3380) --- .../ui/src/components/Snackbar/SnackbarItem.tsx | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/platform/ui/src/components/Snackbar/SnackbarItem.tsx b/platform/ui/src/components/Snackbar/SnackbarItem.tsx index 25b1e0c02..7ed192ffd 100644 --- a/platform/ui/src/components/Snackbar/SnackbarItem.tsx +++ b/platform/ui/src/components/Snackbar/SnackbarItem.tsx @@ -37,15 +37,9 @@ const SnackbarItem = ({ options, onClose }) => { typeClasses[options.type] )} > -
-
- -
+
-
+
{/* */} {options.title && (
@@ -58,6 +52,12 @@ const SnackbarItem = ({ options, onClose }) => {
)}
+
+ +
); From 8eaa1877fd8f3a3b33a91f9c805bd973c74d722f Mon Sep 17 00:00:00 2001 From: Joe Boccanfuso <109477394+jbocce@users.noreply.github.com> Date: Wed, 10 May 2023 12:42:48 -0400 Subject: [PATCH 38/54] fix(DICOM PDF and Video): fixes for local DICOM load and remote data sources (#3374) * fix(DICOM PDF and Video) - added retrieve.directURL for local DICOM load data source; it returns a data URL - fixed various checks for video using transfer syntaxes and SOP class UID with number of frames - added call to 'rendered' endpoint for those data sources that support it; others get BulkDataURI * Added DOC (PDF) and OT (for video in particular) to list of non-image thumbnail modalities. * Fixed broken e2e tests. --- .../default/src/DicomLocalDataSource/index.js | 12 ++++++++++++ .../default/src/DicomWebDataSource/index.js | 10 ++++++++-- extensions/default/src/utils/getDirectURL.js | 18 ++++++++++-------- .../viewports/OHIFCornerstonePdfViewport.tsx | 5 ++--- .../src/getSopClassHandlerModule.js | 13 ++++++++++++- .../viewports/OHIFCornerstoneVideoViewport.tsx | 3 +-- .../PanelStudyBrowserTracking.tsx | 2 ++ .../ThumbnailNoImage/ThumbnailNoImage.tsx | 3 ++- .../cypress/integration/OHIFPdfDisplay.spec.js | 2 +- .../integration/OHIFVideoDisplay.spec.js | 6 ++++-- .../viewer/public/config/local_dcm4chee.js | 1 + .../viewer/src/routes/Local/dicomFileLoader.js | 4 ++++ 12 files changed, 59 insertions(+), 20 deletions(-) diff --git a/extensions/default/src/DicomLocalDataSource/index.js b/extensions/default/src/DicomLocalDataSource/index.js index f10d427ba..d7b3d7106 100644 --- a/extensions/default/src/DicomLocalDataSource/index.js +++ b/extensions/default/src/DicomLocalDataSource/index.js @@ -115,6 +115,18 @@ function createDicomLocalApi(dicomLocalConfig) { }, }, retrieve: { + directURL: params => { + const { instance, tag, defaultType } = params; + + const value = instance[tag]; + if (value instanceof Array && value[0] instanceof ArrayBuffer) { + return URL.createObjectURL( + new Blob([value[0]], { + type: defaultType, + }) + ); + } + }, series: { metadata: async ({ StudyInstanceUID, madeInClient = false } = {}) => { if (!StudyInstanceUID) { diff --git a/extensions/default/src/DicomWebDataSource/index.js b/extensions/default/src/DicomWebDataSource/index.js index c5782375c..01943417e 100644 --- a/extensions/default/src/DicomWebDataSource/index.js +++ b/extensions/default/src/DicomWebDataSource/index.js @@ -178,7 +178,7 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) { * or is already retrieved, or a promise to a URL for such use if a BulkDataURI */ directURL: params => { - return getDirectURL(wadoRoot, params); + return getDirectURL({ wadoRoot, singlepart }, params); }, bulkDataURI: async ({ StudyInstanceUID, BulkDataURI }) => { const options = { @@ -394,7 +394,13 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) { }; // Todo: this needs to be from wado dicom web client return qidoDicomWebClient.retrieveBulkData(options).then(val => { - const ret = (val && val[0]) || undefined; + // There are DICOM PDF cases where the first ArrayBuffer in the array is + // the bulk data and DICOM video cases where the second ArrayBuffer is + // the bulk data. Here we play it safe and do a find. + const ret = + (val instanceof Array && + val.find(arrayBuffer => arrayBuffer?.byteLength)) || + undefined; value.Value = ret; return ret; }); diff --git a/extensions/default/src/utils/getDirectURL.js b/extensions/default/src/utils/getDirectURL.js index e90ff17af..4580b8d30 100644 --- a/extensions/default/src/utils/getDirectURL.js +++ b/extensions/default/src/utils/getDirectURL.js @@ -19,13 +19,13 @@ import { * @returns an absolute URL to the resource, if the absolute URL can be retrieved as singlepart, * or is already retrieved, or a promise to a URL for such use if a BulkDataURI */ -const getDirectURL = (wadoRoot, params) => { +const getDirectURL = (config, params) => { + const { wadoRoot, singlepart } = config; const { instance, tag = 'PixelData', defaultPath = '/pixeldata', defaultType = 'video/mp4', - singlepart = null, singlepart: fetchPart = 'video', } = params; const value = instance[tag]; @@ -53,11 +53,7 @@ const getDirectURL = (wadoRoot, params) => { return undefined; } - const { - StudyInstanceUID, - SeriesInstanceUID, - SOPInstanceUID, - } = instance; + const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = instance; const BulkDataURI = (value && value.BulkDataURI) || `series/${SeriesInstanceUID}/instances/${SOPInstanceUID}${defaultPath}`; @@ -66,7 +62,13 @@ const getDirectURL = (wadoRoot, params) => { const acceptUri = BulkDataURI + (hasAccept ? '' : (hasQuery ? '&' : '?') + `accept=${defaultType}`); - if (BulkDataURI.indexOf('http') === 0) return acceptUri; + if (BulkDataURI.indexOf('http') === 0) { + if (tag === 'PixelData' || tag === 'EncapsulatedDocument') { + return `${wadoRoot}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/instances/${SOPInstanceUID}/rendered`; + } else { + return acceptUri; + } + } if (BulkDataURI.indexOf('/') === 0) { return wadoRoot + acceptUri; } diff --git a/extensions/dicom-pdf/src/viewports/OHIFCornerstonePdfViewport.tsx b/extensions/dicom-pdf/src/viewports/OHIFCornerstonePdfViewport.tsx index 99488a21f..9da1904c1 100644 --- a/extensions/dicom-pdf/src/viewports/OHIFCornerstonePdfViewport.tsx +++ b/extensions/dicom-pdf/src/viewports/OHIFCornerstonePdfViewport.tsx @@ -14,15 +14,14 @@ function OHIFCornerstonePdfViewport({ displaySets }) { useEffect(() => { const load = async () => { - await pdfUrl; - setUrl(pdfUrl); + setUrl(await pdfUrl); }; load(); }, [pdfUrl]); return ( -
+
No online PDF viewer installed
 diff --git a/extensions/dicom-video/src/getSopClassHandlerModule.js b/extensions/dicom-video/src/getSopClassHandlerModule.js index 4be185e74..72fc00884 100644 --- a/extensions/dicom-video/src/getSopClassHandlerModule.js +++ b/extensions/dicom-video/src/getSopClassHandlerModule.js @@ -37,7 +37,18 @@ const _getDisplaySetsFromSeries = ( metadata.AvailableTransferSyntaxUID || metadata.TransferSyntaxUID || metadata['00083002']; - return supportedTransferSyntaxUIDs.includes(tsuid); + + if (supportedTransferSyntaxUIDs.includes(tsuid)) { + return true; + } + + // Assume that an instance with certain SOPClassUID and + // with at least 90 frames (i.e. typically 3 seconds of video) is indeed a video. + return ( + metadata.SOPClassUID === + SOP_CLASS_UIDS.MULTIFRAME_TRUE_COLOR_SECONDARY_CAPTURE_IMAGE_STORAGE && + metadata.NumberOfFrames >= 90 + ); }) .map(instance => { const { diff --git a/extensions/dicom-video/src/viewports/OHIFCornerstoneVideoViewport.tsx b/extensions/dicom-video/src/viewports/OHIFCornerstoneVideoViewport.tsx index 56545b2a0..c6aa80b2f 100644 --- a/extensions/dicom-video/src/viewports/OHIFCornerstoneVideoViewport.tsx +++ b/extensions/dicom-video/src/viewports/OHIFCornerstoneVideoViewport.tsx @@ -14,8 +14,7 @@ function OHIFCornerstoneVideoViewport({ displaySets }) { useEffect(() => { const load = async () => { - await videoUrl; - setUrl(videoUrl); + setUrl(await videoUrl); }; load(); diff --git a/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx b/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx index e81309ce2..ca1f383e2 100644 --- a/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx +++ b/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx @@ -549,6 +549,8 @@ const thumbnailNoImageModalities = [ 'RTSTRUCT', 'RTPLAN', 'RTDOSE', + 'DOC', + 'OT', ]; function _getComponentType(Modality) { diff --git a/platform/ui/src/components/ThumbnailNoImage/ThumbnailNoImage.tsx b/platform/ui/src/components/ThumbnailNoImage/ThumbnailNoImage.tsx index 1a6e24952..83eb44536 100644 --- a/platform/ui/src/components/ThumbnailNoImage/ThumbnailNoImage.tsx +++ b/platform/ui/src/components/ThumbnailNoImage/ThumbnailNoImage.tsx @@ -18,7 +18,7 @@ const ThumbnailNoImage = ({ isActive, }) => { const [collectedProps, drag, dragPreview] = useDrag({ - type: "displayset", + type: 'displayset', item: { ...dragData }, canDrag: function(monitor) { return Object.keys(dragData).length !== 0; @@ -39,6 +39,7 @@ const ThumbnailNoImage = ({ onDoubleClick={onDoubleClick} role="button" tabIndex="0" + data-cy={`study-browser-thumbnail-no-image`} >
diff --git a/platform/viewer/cypress/integration/OHIFPdfDisplay.spec.js b/platform/viewer/cypress/integration/OHIFPdfDisplay.spec.js index 954dca093..8027380f6 100644 --- a/platform/viewer/cypress/integration/OHIFPdfDisplay.spec.js +++ b/platform/viewer/cypress/integration/OHIFPdfDisplay.spec.js @@ -6,7 +6,7 @@ describe('OHIF PDF Display', function() { }); it('checks if series thumbnails are being displayed', function() { - cy.get('[data-cy="study-browser-thumbnail"]') + cy.get('[data-cy="study-browser-thumbnail-no-image"]') .its('length') .should('be.gt', 0); }); diff --git a/platform/viewer/cypress/integration/OHIFVideoDisplay.spec.js b/platform/viewer/cypress/integration/OHIFVideoDisplay.spec.js index b03ec0a42..e312144ee 100644 --- a/platform/viewer/cypress/integration/OHIFVideoDisplay.spec.js +++ b/platform/viewer/cypress/integration/OHIFVideoDisplay.spec.js @@ -5,13 +5,15 @@ describe('OHIF Video Display', function() { }); it('checks if series thumbnails are being displayed', function() { - cy.get('[data-cy="study-browser-thumbnail"]') + cy.get('[data-cy="study-browser-thumbnail-no-image"]') .its('length') .should('be.gt', 1); }); it('performs double-click to load thumbnail in active viewport', () => { - cy.get('[data-cy="study-browser-thumbnail"]:nth-child(2)').dblclick(); + cy.get( + '[data-cy="study-browser-thumbnail-no-image"]:nth-child(2)' + ).dblclick(); //const expectedText = 'Ser: 3'; //cy.get('@viewportInfoBottomLeft').should('contains.text', expectedText); diff --git a/platform/viewer/public/config/local_dcm4chee.js b/platform/viewer/public/config/local_dcm4chee.js index d47c4c34a..682501fff 100644 --- a/platform/viewer/public/config/local_dcm4chee.js +++ b/platform/viewer/public/config/local_dcm4chee.js @@ -32,6 +32,7 @@ window.config = { auth: 'admin:admin', }, dicomUploadEnabled: true, + singlepart: 'pdf,video', }, }, { diff --git a/platform/viewer/src/routes/Local/dicomFileLoader.js b/platform/viewer/src/routes/Local/dicomFileLoader.js index 1188e3169..d9e2ea92c 100644 --- a/platform/viewer/src/routes/Local/dicomFileLoader.js +++ b/platform/viewer/src/routes/Local/dicomFileLoader.js @@ -21,6 +21,10 @@ const DICOMFileLoader = new (class extends FileLoader { dicomData.meta ); + dataset.AvailableTransferSyntaxUID = + dataset.AvailableTransferSyntaxUID || + dataset._meta.TransferSyntaxUID?.Value?.[0]; + return dataset; } })(); From 656f9cf7616ef5492b75ff33bec80ecc4b1b1145 Mon Sep 17 00:00:00 2001 From: dxlin Date: Wed, 10 May 2023 15:04:49 -0400 Subject: [PATCH 39/54] docs(HP): update for sameAs attribute doc (#3383) Update HangingProtocolService doc to include example and instructions to use custom attributes included in @ohif/extension-test. Example shows usage of sameAs for frame of reference check in tmtv hanging protocol. --- .../services/data/HangingProtocolService.md | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/platform/docs/docs/platform/services/data/HangingProtocolService.md b/platform/docs/docs/platform/services/data/HangingProtocolService.md index 21f615824..8343d9745 100644 --- a/platform/docs/docs/platform/services/data/HangingProtocolService.md +++ b/platform/docs/docs/platform/services/data/HangingProtocolService.md @@ -310,3 +310,51 @@ viewportOptions: { // This is the value returned if the above doesn't return anything defaultValue: { index: 5 }, ``` + +### Included Custom Attributes + +A few custom attributes are included under @ohif/extension-test, these are namely: +*sameAs +*maxNumImageFrames +*numberOfDisplaySets + +To use these included custom attributes, the extension will need to be enabled under platform/viewer/pluginConfig.json: + +```javascript +{ + "extensions": [ + ... + { + "packageName": "@ohif/extension-test", + "version": "0.0.1" + }, + ... + ] +} + ``` + +Furthermore, the extension will also need to be included under extensionDependencies in the desired mode (e.g. modes/tmtv/src/index.js): + +```javascript +const extensionDependencies = { + '@ohif/extension-default': '^3.0.0', + '@ohif/extension-cornerstone': '^3.0.0', + '@ohif/extension-tmtv': '^3.0.0', + '@ohif/extension-test': '^0.0.1', + }; + ``` + +The below example modifies the included hanging protocol (extensions/tmtv/src/getHangingProtocolModule.js) and uses the sameAs attribute included in the @ohif/extension-test extension to check that the selected PT has the same frame of reference as the CT: + +```javascript +ptDisplaySet: { + ... + seriesMatchingRules: [ + { + attribute: 'sameAs', + sameAttribute: 'FrameOfReferenceUID', + sameDisplaySetId: 'ctDisplaySet', + required: true, + }, + ... +``` From cba57a1b65b6acffce6391aabd6a929faa85f722 Mon Sep 17 00:00:00 2001 From: Joe Boccanfuso <109477394+jbocce@users.noreply.github.com> Date: Thu, 11 May 2023 09:52:32 -0400 Subject: [PATCH 40/54] fix(UI): fixed results per page select menu (#3384) --- platform/ui/src/components/Select/Select.css | 22 +++++++------------ platform/ui/src/components/Select/Select.tsx | 2 +- .../StudyListPagination.tsx | 2 +- .../viewer/src/routes/WorkList/WorkList.tsx | 20 +++++++++-------- 4 files changed, 21 insertions(+), 25 deletions(-) diff --git a/platform/ui/src/components/Select/Select.css b/platform/ui/src/components/Select/Select.css index 34a8e96a7..5e407bd01 100644 --- a/platform/ui/src/components/Select/Select.css +++ b/platform/ui/src/components/Select/Select.css @@ -52,18 +52,19 @@ border-radius: 6px; } -.css-4ljt47-MenuList { +.ohif-select .customSelect__menu-list { overflow-x: hidden !important; margin-right: 4px; margin-top: 4px; padding-top: 0px !important; } -.css-4ljt47-MenuList::-webkit-scrollbar { + +.ohif-select .customSelect__menu-list::-webkit-scrollbar { width: 6px; border-radius: 10px; } -.css-4ljt47-MenuList::-webkit-scrollbar-thumb { +.ohif-select .customSelect__menu-list::-webkit-scrollbar-thumb { background-color: #0944b3; border-radius: 10px; } @@ -71,26 +72,19 @@ .customSelect__option:focus { background-color: #0944b391 !important; } -.customSelect__option label { + +.ohif-select .customSelect__option, .ohif-select .customSelect__option label { color: #d6d6d6; font-size: 14px; display: flex; align-items: center; } -.css-1n7v3ny-option { - background-color: #0944b391 !important; -} - -.css-1n7v3ny-option:focus { - background-color: #0944b391 !important; -} - -.customSelect__option:hover { +.ohif-select .customSelect__option:hover { background-color: #0944b391; } -.css-26l3qy-menu { +.ohif-select .customSelect__menu { border: 2px solid #0944b3; border-radius: 6px; background-color: #151515 !important; diff --git a/platform/ui/src/components/Select/Select.tsx b/platform/ui/src/components/Select/Select.tsx index aab80f349..2835cb23a 100644 --- a/platform/ui/src/components/Select/Select.tsx +++ b/platform/ui/src/components/Select/Select.tsx @@ -77,7 +77,7 @@ const Select = ({ inputId={`input-${id}`} className={classnames( className, - 'flex flex-col flex-1 customSelect__wrapper' + 'ohif-select flex flex-col flex-1 customSelect__wrapper' )} data-cy={`input-${id}`} classNamePrefix="customSelect" diff --git a/platform/ui/src/components/StudyListPagination/StudyListPagination.tsx b/platform/ui/src/components/StudyListPagination/StudyListPagination.tsx index a21a4a8b7..87e21cf3b 100644 --- a/platform/ui/src/components/StudyListPagination/StudyListPagination.tsx +++ b/platform/ui/src/components/StudyListPagination/StudyListPagination.tsx @@ -36,7 +36,7 @@ const StudyListPagination = ({