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feat: Add CS3D WSI and Video Viewports and add annotation navigation for MPR (#4182)

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Bill Wallace authored and GitHub committed 2024-08-15 14:36:53 -04:00
1 parent b12e0211d4
commit 7599ec9421
65 files changed
+781 -513
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extensions/cornerstone-dicom-sr/package.json
+3 -3
View File
@@ -46,9 +46,9 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.82.0",
"@cornerstonejs/core": "^1.82.0",
"@cornerstonejs/tools": "^1.82.0",
"@cornerstonejs/adapters": "^1.82.4",
"@cornerstonejs/core": "^1.82.4",
"@cornerstonejs/tools": "^1.82.4",
"classnames": "^2.3.2"
}
}
extensions/cornerstone-dynamic-volume/package.json
+3 -3
View File
@@ -42,9 +42,9 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/core": "^1.82.0",
"@cornerstonejs/streaming-image-volume-loader": "^1.82.0",
"@cornerstonejs/tools": "^1.82.0",
"@cornerstonejs/core": "^1.82.4",
"@cornerstonejs/streaming-image-volume-loader": "^1.82.4",
"@cornerstonejs/tools": "^1.82.4",
"classnames": "^2.3.2"
}
}
extensions/cornerstone/package.json
+5 -5
View File
@@ -38,7 +38,7 @@
"@cornerstonejs/codec-libjpeg-turbo-8bit": "^1.2.2",
"@cornerstonejs/codec-openjpeg": "^1.2.2",
"@cornerstonejs/codec-openjph": "^2.4.2",
"@cornerstonejs/dicom-image-loader": "^1.82.0",
"@cornerstonejs/dicom-image-loader": "^1.82.4",
"@icr/polyseg-wasm": "^0.4.0",
"@ohif/core": "3.9.0-beta.77",
"@ohif/ui": "3.9.0-beta.77",
@@ -55,10 +55,10 @@
},
"dependencies": {
"@babel/runtime": "^7.20.13",
"@cornerstonejs/adapters": "^1.82.0",
"@cornerstonejs/core": "^1.82.0",
"@cornerstonejs/streaming-image-volume-loader": "^1.82.0",
"@cornerstonejs/tools": "^1.82.0",
"@cornerstonejs/adapters": "^1.82.4",
"@cornerstonejs/core": "^1.82.4",
"@cornerstonejs/streaming-image-volume-loader": "^1.82.4",
"@cornerstonejs/tools": "^1.82.4",
"@icr/polyseg-wasm": "^0.4.0",
"@kitware/vtk.js": "30.4.1",
"html2canvas": "^1.4.1",
extensions/cornerstone/src/Viewport/OHIFCornerstoneViewport.tsx
+26 -119
View File
@@ -2,24 +2,17 @@ import React, { useEffect, useRef, useCallback, useState } from 'react';
import { useResizeDetector } from 'react-resize-detector';
import PropTypes from 'prop-types';
import * as cs3DTools from '@cornerstonejs/tools';
import {
Enums,
eventTarget,
getEnabledElement,
StackViewport,
utilities as csUtils,
} from '@cornerstonejs/core';
import { Enums, eventTarget, getEnabledElement } from '@cornerstonejs/core';
import { MeasurementService } from '@ohif/core';
import { Notification, useViewportDialog, AllInOneMenu } from '@ohif/ui';
import { IStackViewport, IVolumeViewport } from '@cornerstonejs/core/dist/esm/types';
import type { Types as csTypes } from '@cornerstonejs/core';
import { setEnabledElement } from '../state';
import './OHIFCornerstoneViewport.css';
import CornerstoneOverlays from './Overlays/CornerstoneOverlays';
import getSOPInstanceAttributes from '../utils/measurementServiceMappings/utils/getSOPInstanceAttributes';
import CinePlayer from '../components/CinePlayer';
import { Types } from '@ohif/core';
import type { Types } from '@ohif/core';
import OHIFViewportActionCorners from '../components/OHIFViewportActionCorners';
import { getWindowLevelActionMenu } from '../components/WindowLevelActionMenu/getWindowLevelActionMenu';
@@ -106,6 +99,7 @@ const OHIFCornerstoneViewport = React.memo((props: withAppTypes) => {
viewportOptions,
displaySetOptions,
servicesManager,
commandsManager,
onElementEnabled,
// eslint-disable-next-line react/prop-types
onElementDisabled,
@@ -149,14 +143,12 @@ const OHIFCornerstoneViewport = React.memo((props: withAppTypes) => {
const [appConfig] = useAppConfig();
const {
measurementService,
displaySetService,
toolbarService,
toolGroupService,
syncGroupService,
cornerstoneViewportService,
cornerstoneCacheService,
viewportGridService,
stateSyncService,
viewportActionCornersService,
} = servicesManager.services;
@@ -370,24 +362,12 @@ const OHIFCornerstoneViewport = React.memo((props: withAppTypes) => {
}
const unsubscribeFromJumpToMeasurementEvents = _subscribeToJumpToMeasurementEvents(
measurementService,
displaySetService,
elementRef,
viewportId,
displaySets,
viewportGridService,
cornerstoneViewportService
servicesManager
);
_checkForCachedJumpToMeasurementEvents(
measurementService,
displaySetService,
elementRef,
viewportId,
displaySets,
viewportGridService,
cornerstoneViewportService
);
_checkForCachedJumpToMeasurementEvents(elementRef, viewportId, displaySets, servicesManager);
return () => {
unsubscribeFromJumpToMeasurementEvents();
@@ -471,15 +451,9 @@ const OHIFCornerstoneViewport = React.memo((props: withAppTypes) => {
);
}, areEqual);
function _subscribeToJumpToMeasurementEvents(
measurementService,
displaySetService,
elementRef,
viewportId,
displaySets,
viewportGridService,
cornerstoneViewportService
) {
function _subscribeToJumpToMeasurementEvents(elementRef, viewportId, servicesManager) {
const { measurementService, cornerstoneViewportService } = servicesManager.services;
const { unsubscribe } = measurementService.subscribe(
MeasurementService.EVENTS.JUMP_TO_MEASUREMENT_VIEWPORT,
props => {
@@ -491,27 +465,17 @@ function _subscribeToJumpToMeasurementEvents(
if (cacheJumpToMeasurementEvent.cornerstoneViewport === undefined) {
// Decide on which viewport should handle this
cacheJumpToMeasurementEvent.cornerstoneViewport =
cornerstoneViewportService.getViewportIdToJump(
jumpId,
measurement.displaySetInstanceUID,
{
referencedImageId:
measurement.referencedImageId || measurement.metadata?.referencedImageId,
}
);
cornerstoneViewportService.getViewportIdToJump(jumpId, {
displaySetInstanceUID: measurement.displaySetInstanceUID,
...measurement.metadata,
referencedImageId:
measurement.referencedImageId || measurement.metadata?.referencedImageId,
});
}
if (cacheJumpToMeasurementEvent.cornerstoneViewport !== viewportId) {
return;
}
_jumpToMeasurement(
measurement,
elementRef,
viewportId,
measurementService,
displaySetService,
viewportGridService,
cornerstoneViewportService
);
_jumpToMeasurement(measurement, elementRef, viewportId, servicesManager);
}
);
@@ -520,13 +484,10 @@ function _subscribeToJumpToMeasurementEvents(
// Check if there is a queued jumpToMeasurement event
function _checkForCachedJumpToMeasurementEvents(
measurementService,
displaySetService,
elementRef,
viewportId,
displaySets,
viewportGridService,
cornerstoneViewportService
servicesManager
) {
if (!cacheJumpToMeasurementEvent) {
return;
@@ -544,37 +505,15 @@ function _checkForCachedJumpToMeasurementEvents(
const { measurement } = cacheJumpToMeasurementEvent;
if (measurement && elementRef) {
if (displaysUIDs.includes(measurement?.displaySetInstanceUID)) {
_jumpToMeasurement(
measurement,
elementRef,
viewportId,
measurementService,
displaySetService,
viewportGridService,
cornerstoneViewportService
);
_jumpToMeasurement(measurement, elementRef, viewportId, servicesManager);
}
}
}
function _jumpToMeasurement(
measurement,
targetElementRef,
viewportId,
measurementService,
displaySetService,
viewportGridService,
cornerstoneViewportService
) {
function _jumpToMeasurement(measurement, targetElementRef, viewportId, servicesManager) {
const { viewportGridService } = servicesManager.services;
const targetElement = targetElementRef.current;
const { displaySetInstanceUID, SOPInstanceUID, frameNumber } = measurement;
if (!SOPInstanceUID) {
console.warn('cannot jump in a non-acquisition plane measurements yet');
return;
}
const referencedDisplaySet = displaySetService.getDisplaySetByUID(displaySetInstanceUID);
// Todo: setCornerstoneMeasurementActive should be handled by the toolGroupManager
// to set it properly
@@ -586,47 +525,15 @@ function _jumpToMeasurement(
if (enabledElement) {
// See how the jumpToSlice() of Cornerstone3D deals with imageIdx param.
const viewport = enabledElement.viewport as IStackViewport | IVolumeViewport;
const viewport = enabledElement.viewport as csTypes.IStackViewport | csTypes.IVolumeViewport;
let imageIdIndex = 0;
let viewportCameraDirectionMatch = true;
if (viewport instanceof StackViewport) {
const imageIds = viewport.getImageIds();
imageIdIndex = imageIds.findIndex(imageId => {
const { SOPInstanceUID: aSOPInstanceUID, frameNumber: aFrameNumber } =
getSOPInstanceAttributes(imageId);
return aSOPInstanceUID === SOPInstanceUID && (!frameNumber || frameNumber === aFrameNumber);
});
} 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: measurementViewPlane } = measurement.metadata;
imageIdIndex = referencedDisplaySet.images.findIndex(
i => i.SOPInstanceUID === SOPInstanceUID
);
// the index is reversed in the volume viewport
// imageIdIndex = referencedDisplaySet.images.length - 1 - imageIdIndex;
const { viewPlaneNormal: viewportViewPlane } = viewport.getCamera();
// should compare abs for both planes since the direction can be flipped
if (
measurementViewPlane &&
!csUtils.isEqual(measurementViewPlane.map(Math.abs), viewportViewPlane.map(Math.abs))
) {
viewportCameraDirectionMatch = false;
}
}
if (!viewportCameraDirectionMatch || imageIdIndex === -1) {
const { metadata } = measurement;
if (!viewport.isReferenceViewable(metadata, { withNavigation: true, withOrientation: true })) {
console.log("Reference isn't viewable, postponing until updated");
return;
}
cs3DTools.utilities.jumpToSlice(targetElement, {
imageIndex: imageIdIndex,
});
viewport.setViewReference(metadata);
cs3DTools.annotation.selection.setAnnotationSelected(measurement.uid);
// Jump to measurement consumed, remove.
extensions/cornerstone/src/Viewport/Overlays/ViewportImageScrollbar.tsx
+20 -47
View File
@@ -43,67 +43,40 @@ function CornerstoneImageScrollbar({
return;
}
if (viewportData.viewportType === Enums.ViewportType.STACK) {
const imageIndex = viewport.getCurrentImageIdIndex();
const imageIndex = viewport.getCurrentImageIdIndex();
const numberOfSlices = viewport.getNumberOfSlices();
setImageSliceData({
imageIndex: imageIndex,
numberOfSlices: viewportData.data[0].imageIds.length,
});
return;
}
if (viewportData.viewportType === Enums.ViewportType.ORTHOGRAPHIC) {
const sliceData = utilities.getImageSliceDataForVolumeViewport(
viewport as Types.IVolumeViewport
);
if (!sliceData) {
return;
}
const { imageIndex, numberOfSlices } = sliceData;
setImageSliceData({ imageIndex, numberOfSlices });
}
setImageSliceData({
imageIndex: imageIndex,
numberOfSlices,
});
}, [viewportId, viewportData]);
useEffect(() => {
if (viewportData?.viewportType !== Enums.ViewportType.STACK) {
if (!viewportData) {
return;
}
const { viewportType } = viewportData;
const eventId =
(viewportType === Enums.ViewportType.STACK && Enums.Events.STACK_VIEWPORT_SCROLL) ||
(viewportType === Enums.ViewportType.ORTHOGRAPHIC && Enums.Events.VOLUME_NEW_IMAGE) ||
Enums.Events.IMAGE_RENDERED;
const updateStackIndex = event => {
const { newImageIdIndex } = event.detail;
const updateIndex = event => {
const viewport = cornerstoneViewportService.getCornerstoneViewport(viewportId);
const { imageIndex, newImageIdIndex = imageIndex } = event.detail;
const numberOfSlices = viewport.getNumberOfSlices();
// find the index of imageId in the imageIds
setImageSliceData({
imageIndex: newImageIdIndex,
numberOfSlices: viewportData.data[0].imageIds.length,
numberOfSlices,
});
};
element.addEventListener(Enums.Events.STACK_VIEWPORT_SCROLL, updateStackIndex);
element.addEventListener(eventId, updateIndex);
return () => {
element.removeEventListener(Enums.Events.STACK_VIEWPORT_SCROLL, updateStackIndex);
};
}, [viewportData, element]);
useEffect(() => {
if (viewportData?.viewportType !== Enums.ViewportType.ORTHOGRAPHIC) {
return;
}
const updateVolumeIndex = event => {
const { imageIndex, numberOfSlices } = event.detail;
// find the index of imageId in the imageIds
setImageSliceData({ imageIndex, numberOfSlices });
};
element.addEventListener(Enums.Events.VOLUME_NEW_IMAGE, updateVolumeIndex);
return () => {
element.removeEventListener(Enums.Events.VOLUME_NEW_IMAGE, updateVolumeIndex);
element.removeEventListener(eventId, updateIndex);
};
}, [viewportData, element]);
@@ -112,7 +85,7 @@ function CornerstoneImageScrollbar({
onChange={evt => onImageScrollbarChange(evt, viewportId)}
max={imageSliceData.numberOfSlices ? imageSliceData.numberOfSlices - 1 : 0}
height={scrollbarHeight}
value={imageSliceData.imageIndex}
value={imageSliceData.imageIndex || 0}
/>
);
}
extensions/dicom-microscopy/src/DicomMicroscopySopClassHandler.js → extensions/cornerstone/src/getSopClassHandlerModule.js
+52 -3
View File
@@ -1,13 +1,19 @@
import OHIF from '@ohif/core';
import { utilities as csUtils, Enums as csEnums } from '@cornerstonejs/core';
import dcmjs from 'dcmjs';
import { dicomWebUtils } from '@ohif/extension-default';
const { MetadataModules } = csEnums;
const { utils } = OHIF;
const { denaturalizeDataset } = dcmjs.data.DicomMetaDictionary;
const { transferDenaturalizedDataset, fixMultiValueKeys } = dicomWebUtils;
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';
'@ohif/extension-cornerstone.sopClassHandlerModule.DicomMicroscopySopClassHandler';
function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager) {
// If the series has no instances, stop here
@@ -27,6 +33,7 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
}
}
let imageIdForThumbnail = null;
const dataSource = extensionManager.getActiveDataSource()[0];
if (singleFrameInstance) {
if (currentFrames == 1) {
// Not all DICOM server implementations support thumbnail service,
@@ -35,7 +42,6 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
}
if (!imageIdForThumbnail) {
// use the thumbnail service provided by DICOM server
const dataSource = extensionManager.getActiveDataSource()[0];
imageIdForThumbnail = dataSource.getImageIdsForInstance({
instance: singleFrameInstance,
thumbnail: true,
@@ -83,6 +89,7 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
const displaySet = {
plugin: 'microscopy',
Modality: 'SM',
viewportType: csEnums.ViewportType.WholeSlide,
altImageText: 'Microscopy',
displaySetInstanceUID: utils.guid(),
SOPInstanceUID,
@@ -102,13 +109,51 @@ function _getDisplaySetsFromSeries(instances, servicesManager, extensionManager)
numInstances: 1,
imageIdForThumbnail, // thumbnail image
others: instances, // all other level instances in the image Pyramid
instances,
othersFrameOfReferenceUID,
imageIds: instances.map(instance => instance.imageId),
};
// The microscopy viewer directly accesses the metadata already loaded, and
// uses the DICOMweb client library directly for loading, so it has to be
// provided here.
const dicomWebClient = dataSource.retrieve.getWadoDicomWebClient?.();
const instanceMap = new Map();
instances.forEach(instance => instanceMap.set(instance.imageId, instance));
if (dicomWebClient) {
const webClient = Object.create(dicomWebClient);
// This replaces just the dicom web metadata call with one which retrieves
// internally.
webClient.getDICOMwebMetadata = getDICOMwebMetadata.bind(webClient, instanceMap);
csUtils.genericMetadataProvider.addRaw(displaySet.imageIds[0], {
type: MetadataModules.WADO_WEB_CLIENT,
metadata: webClient,
});
} else {
// Might have some other way of getting the data in the future or internally?
// throw new Error('Unable to provide a DICOMWeb client library, microscopy will fail to view');
}
return [displaySet];
}
export default function getDicomMicroscopySopClassHandler({ servicesManager, extensionManager }) {
/**
* This method provides access to the internal DICOMweb metadata, used to avoid
* refetching the DICOMweb data. It gets assigned as a member function to the
* dicom web client.
*/
function getDICOMwebMetadata(instanceMap, imageId) {
const instance = instanceMap.get(imageId);
if (!instance) {
console.warn('Metadata not already found for', imageId, 'in', instanceMap);
return this.super.getDICOMwebMetadata(imageId);
}
return transferDenaturalizedDataset(
denaturalizeDataset(fixMultiValueKeys(instanceMap.get(imageId)))
);
}
export function getDicomMicroscopySopClassHandler({ servicesManager, extensionManager }) {
const getDisplaySetsFromSeries = instances => {
return _getDisplaySetsFromSeries(instances, servicesManager, extensionManager);
};
@@ -119,3 +164,7 @@ export default function getDicomMicroscopySopClassHandler({ servicesManager, ext
getDisplaySetsFromSeries,
};
}
export function getSopClassHandlerModule(params) {
return [getDicomMicroscopySopClassHandler(params)];
}
extensions/cornerstone/src/index.tsx
+2
View File
@@ -39,6 +39,7 @@ import ActiveViewportWindowLevel from './components/ActiveViewportWindowLevel';
import getSOPInstanceAttributes from './utils/measurementServiceMappings/utils/getSOPInstanceAttributes';
import { findNearbyToolData } from './utils/findNearbyToolData';
import { createFrameViewSynchronizer } from './synchronizers/frameViewSynchronizer';
import { getSopClassHandlerModule } from './getSopClassHandlerModule';
const { helpers: volumeLoaderHelpers } = csStreamingImageVolumeLoader;
const { getDynamicVolumeInfo } = volumeLoaderHelpers ?? {};
@@ -218,6 +219,7 @@ const cornerstoneExtension: Types.Extensions.Extension = {
},
];
},
getSopClassHandlerModule,
};
export type { PublicViewportOptions };
extensions/cornerstone/src/services/CornerstoneCacheService/CornerstoneCacheService.ts
+36 -11
View File
@@ -32,7 +32,7 @@ class CornerstoneCacheService {
}
public async createViewportData(
displaySets: unknown[],
displaySets: Types.DisplaySet[],
viewportOptions: Record<string, unknown>,
dataSource: unknown,
initialImageIndex?: number
@@ -55,23 +55,29 @@ class CornerstoneCacheService {
viewportOptions.viewportType = viewportType;
}
const cs3DViewportType = getCornerstoneViewportType(viewportType);
const cs3DViewportType = getCornerstoneViewportType(viewportType, displaySets);
let viewportData: StackViewportData | VolumeViewportData;
if (cs3DViewportType === Enums.ViewportType.STACK) {
viewportData = await this._getStackViewportData(
dataSource,
displaySets,
initialImageIndex,
cs3DViewportType
);
}
if (
cs3DViewportType === Enums.ViewportType.ORTHOGRAPHIC ||
cs3DViewportType === Enums.ViewportType.VOLUME_3D
) {
viewportData = await this._getVolumeViewportData(dataSource, displaySets, cs3DViewportType);
} else if (cs3DViewportType === Enums.ViewportType.STACK) {
// Everything else looks like a stack
viewportData = await this._getStackViewportData(
dataSource,
displaySets,
initialImageIndex,
cs3DViewportType
);
} else {
viewportData = await this._getOtherViewportData(
dataSource,
displaySets,
initialImageIndex,
cs3DViewportType
);
}
viewportData.viewportType = cs3DViewportType;
@@ -143,6 +149,25 @@ class CornerstoneCacheService {
return newViewportData;
}
private async _getOtherViewportData(
dataSource,
displaySets,
_initialImageIndex,
viewportType: Enums.ViewportType
): Promise<StackViewportData> {
// TODO - handle overlays and secondary display sets, but for now assume
// the 1st display set is the one of interest
const [displaySet] = displaySets;
if (!displaySet.imageIds) {
displaySet.imagesIds = this._getCornerstoneStackImageIds(displaySet, dataSource);
}
const { imageIds: data, viewportType: dsViewportType } = displaySet;
return {
viewportType: dsViewportType || viewportType,
data: displaySets,
};
}
private async _getStackViewportData(
dataSource,
displaySets,
extensions/cornerstone/src/services/ViewportService/CornerstoneViewportService.ts
+110 -62
View File
@@ -65,6 +65,14 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
this.viewportGridResizeObserver = null;
this.servicesManager = servicesManager;
}
hangingProtocolService: unknown;
viewportsInfo: unknown;
sceneVolumeInputs: unknown;
viewportDivElements: unknown;
ViewportPropertiesMap: unknown;
volumeUIDs: unknown;
displaySetsNeedRerendering: unknown;
viewportDisplaySets: unknown;
/**
* Adds the HTML element to the viewportService
@@ -166,17 +174,18 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
*
* @param viewportId - The ID of the viewport.
* @param presentations - The presentations to apply to the viewport.
* @param viewportInfo - Contains a view reference for immediate application
*/
public setPresentations(viewportId: string, presentations?: Presentations): void {
public setPresentations(
viewportId: string,
presentations?: Presentations,
viewportInfo?: ViewportInfo
): void {
const viewport = this.getCornerstoneViewport(viewportId) as
| Types.IStackViewport
| Types.IVolumeViewport;
if (!viewport) {
return;
}
if (!presentations) {
if (!viewport || !presentations) {
return;
}
@@ -196,17 +205,12 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
}
}
if (positionPresentation) {
const { viewPlaneNormal, viewUp, zoom, pan } = positionPresentation.presentation;
viewport.setCamera({ viewPlaneNormal, viewUp });
if (zoom !== undefined) {
viewport.setZoom(zoom);
}
if (pan !== undefined) {
viewport.setPan(pan);
}
const viewRef = viewportInfo?.getViewReference() || positionPresentation?.viewReference;
if (viewRef) {
viewport.setViewReference(viewRef);
}
if (positionPresentation?.position) {
viewport.setViewPresentation(positionPresentation.position);
}
}
@@ -235,21 +239,11 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
return;
}
const { viewPlaneNormal, viewUp } = csViewport.getCamera();
const initialImageIndex = csViewport.getCurrentImageIdIndex() || 0;
const zoom = csViewport.getZoom();
const pan = csViewport.getPan();
return {
id: positionPresentationId,
viewportType: viewportInfo.getViewportType(),
presentation: {
initialImageIndex,
viewUp,
viewPlaneNormal,
zoom,
pan,
},
viewReference: csViewport.getViewReference(),
position: csViewport.getViewPresentation({ pan: true, zoom: true }),
};
}
@@ -428,7 +422,14 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
// override the viewportOptions and displaySetOptions with the public ones
// since those are the newly set ones, we set them here so that it handles defaults
const displaySetOptions = viewportInfo.setPublicDisplaySetOptions(publicDisplaySetOptions);
const viewportOptions = viewportInfo.setPublicViewportOptions(publicViewportOptions);
// Specify an over-ride for the viewport type, even though it is in the public
// viewport options, because the one in the public viewport options is a suggestion
// for initial view, whereas the one in viewportData is a requirement based on the
// type of data being displayed.
const viewportOptions = viewportInfo.setPublicViewportOptions(
publicViewportOptions,
viewportData.viewportType
);
const element = viewportInfo.getElement();
const type = viewportInfo.getViewportType();
@@ -518,35 +519,80 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
/**
* Looks through the viewports to see if the specified measurement can be
* displayed in one of the viewports.
* displayed in one of the viewports. This function tries to get a "best fit"
* viewport to display the image in where it matches, in order:
* * Active viewport that can be navigated to the given image without orientation change
* * Other viewport that can be navigated to the given image without orientation change
* * Active viewport that can change orientation to display the image
* * Other viewport that can change orientation to display the image
*
* @param measurement
* The measurement that is desired to view.
* It returns `null` otherwise, indicating that a viewport needs display set/type
* changes in order to display the image.
*
* Notes:
* * If the display set is displayed in multiple viewports all needing orientation change,
* then the active one or first one listed will be modified. This can create unexpected
* behaviour for MPR views.
* * If the image is contained in multiple display sets, then the first one
* found will be navigated (active first, followed by first found)
*
* @param measurement - The measurement that is desired to view.
* @param activeViewportId - the index that was active at the time the jump
* was initiated.
* @return the viewportId that the measurement should be displayed in.
*/
public getViewportIdToJump(
activeViewportId: string,
displaySetInstanceUID: string,
cameraProps: unknown
): string {
const viewportInfo = this.getViewportInfo(activeViewportId);
if (viewportInfo.getViewportType() === csEnums.ViewportType.VOLUME_3D) {
return null;
}
const { referencedImageId } = cameraProps;
if (viewportInfo?.contains(displaySetInstanceUID, referencedImageId)) {
public getViewportIdToJump(activeViewportId: string, metadata): string {
// First check if the active viewport can just be navigated to show the given item
const activeViewport = this.getCornerstoneViewport(activeViewportId);
if (activeViewport.isReferenceViewable(metadata, { withNavigation: true })) {
return activeViewportId;
}
return (
[...this.viewportsById.values()].find(viewportInfo =>
viewportInfo.contains(displaySetInstanceUID, referencedImageId)
)?.viewportId ?? null
);
// Next, see if any viewport could be navigated to show the given item,
// without considering orientation changes.
for (const id of this.viewportsById.keys()) {
const viewport = this.getCornerstoneViewport(id);
if (viewport?.isReferenceViewable(metadata, { withNavigation: true })) {
return id;
}
}
// No viewport is in the right display set/orientation to show this, so see if
// the active viewport could change orientations to show this
if (
activeViewport.isReferenceViewable(metadata, { withNavigation: true, withOrientation: true })
) {
return activeViewportId;
}
// See if any viewport could show this with an orientation change
for (const id of this.viewportsById.keys()) {
const viewport = this.getCornerstoneViewport(id);
if (
viewport?.isReferenceViewable(metadata, { withNavigation: true, withOrientation: true })
) {
return id;
}
}
// No luck, need to update the viewport itself
return null;
}
/**
* Sets the image data for the given viewport.
*/
private async _setOtherViewport(
viewport: Types.IStackViewport,
viewportData: StackViewportData,
viewportInfo: ViewportInfo,
_presentations: Presentations = {}
): Promise<void> {
const [displaySet] = viewportData.data;
return viewport.setDataIds(displaySet.imageIds, {
groupId: displaySet.displaySetInstanceUID,
viewReference: viewportInfo.getViewReference(),
});
}
private async _setStackViewport(
@@ -566,6 +612,9 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
const { initialImageIndex, imageIds } = viewportData.data[0];
// Use the slice index from any provided view reference, as the view reference
// is being used to navigate to the initial view position for measurement
// navigation and other navigation forcing specific views.
let initialImageIndexToUse =
presentations?.positionPresentation?.initialImageIndex ?? initialImageIndex;
@@ -586,20 +635,15 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
properties.voiRange = { lower, upper };
}
if (voiInverted !== undefined) {
properties.invert = voiInverted;
}
if (colormap !== undefined) {
properties.colormap = colormap;
}
properties.invert = voiInverted ?? properties.invert;
properties.colormap = colormap ?? properties.colormap;
}
this._handleOverlays(viewport);
return viewport.setStack(imageIds, initialImageIndexToUse).then(() => {
viewport.setProperties({ ...properties });
this.setPresentations(viewport.id, presentations);
this.setPresentations(viewport.id, presentations, viewportInfo);
if (displayArea) {
viewport.setDisplayArea(displayArea);
}
@@ -750,7 +794,6 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
const displaySetUIDs = viewportGridService.getDisplaySetsUIDsForViewport(viewport.id);
const displaySet = displaySetService.getDisplaySetByUID(displaySetUIDs[0]);
const displaySetModality = displaySet?.Modality;
// Todo: use presentations states
const volumesProperties = volumeInputArray.map((volumeInput, index) => {
const { volumeId } = volumeInput;
@@ -786,7 +829,7 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
viewport.setProperties(properties, volumeId);
});
this.setPresentations(viewport.id, presentations);
this.setPresentations(viewport.id, presentations, viewportInfo);
this._handleOverlays(viewport);
@@ -976,7 +1019,12 @@ class CornerstoneViewportService extends PubSubService implements IViewportServi
);
}
throw new Error('Unknown viewport type');
return this._setOtherViewport(
viewport as Types.IViewport,
viewportData as StackViewportData,
viewportInfo,
presentations
);
}
/**
extensions/cornerstone/src/services/ViewportService/Viewport.ts
+25 -14
View File
@@ -31,6 +31,9 @@ export type ViewportOptions = {
displayArea?: Types.DisplayArea;
syncGroups?: SyncGroup[];
initialImageOptions?: InitialImageOptions;
rotation?: number;
flipHorizontal?: boolean;
viewReference?: Types.ViewReference;
customViewportProps?: Record<string, unknown>;
/*
* Allows drag and drop of display sets not matching viewport options, but
@@ -49,6 +52,8 @@ export type PublicViewportOptions = {
background?: Types.Point3;
displayArea?: Types.DisplayArea;
syncGroups?: SyncGroup[];
rotation?: number;
flipHorizontal?: boolean;
initialImageOptions?: InitialImageOptions;
customViewportProps?: Record<string, unknown>;
allowUnmatchedView?: boolean;
@@ -130,6 +135,7 @@ class ViewportInfo {
private displaySetOptions: Array<DisplaySetOptions>;
private viewportData: StackViewportData | VolumeViewportData;
private renderingEngineId: string;
private viewReference: Types.ViewReference;
constructor(viewportId: string) {
this.viewportId = viewportId;
@@ -201,6 +207,10 @@ class ViewportInfo {
return this.viewportId;
}
public getViewReference(): Types.ViewReference {
return this.viewportOptions?.viewReference;
}
public setPublicDisplaySetOptions(
publicDisplaySetOptions: PublicDisplaySetOptions[] | DisplaySetSelector[]
): Array<DisplaySetOptions> {
@@ -232,21 +242,22 @@ class ViewportInfo {
return viewportData.data.displaySetInstanceUID === displaySetInstanceUID;
}
public setPublicViewportOptions(viewportOptionsEntry: PublicViewportOptions): ViewportOptions {
let viewportType = viewportOptionsEntry.viewportType;
const { toolGroupId = DEFAULT_TOOLGROUP_ID, presentationIds } = viewportOptionsEntry;
let orientation;
/**
*
* @param viewportOptionsEntry - the base values for the options
* @param viewportTypeDisplaySet - allows overriding the viewport type
*/
public setPublicViewportOptions(
viewportOptionsEntry: PublicViewportOptions,
viewportTypeDisplaySet?: string
): ViewportOptions {
const ohifViewportType = viewportTypeDisplaySet || viewportOptionsEntry.viewportType || STACK;
const { presentationIds } = viewportOptionsEntry;
let { toolGroupId = DEFAULT_TOOLGROUP_ID } = viewportOptionsEntry;
// Just assign the orientation for any viewport type and let the viewport deal with it
const orientation = getCornerstoneOrientation(viewportOptionsEntry.orientation);
if (!viewportType) {
viewportType = getCornerstoneViewportType(STACK);
} else {
viewportType = getCornerstoneViewportType(viewportOptionsEntry.viewportType);
}
// map SAGITTAL, AXIAL, CORONAL orientation to be used by cornerstone
if (viewportOptionsEntry.viewportType?.toLowerCase() !== STACK) {
orientation = getCornerstoneOrientation(viewportOptionsEntry.orientation);
}
const viewportType = getCornerstoneViewportType(ohifViewportType);
if (!toolGroupId) {
toolGroupId = DEFAULT_TOOLGROUP_ID;
extensions/cornerstone/src/types/CornerstoneCacheService.ts
-1
View File
@@ -9,7 +9,6 @@ type StackData = {
isCompositeStack?: boolean;
imageIds: string[];
frameRate?: number;
isClip?: boolean;
initialImageIndex?: number | string | null;
};
extensions/cornerstone/src/types/Presentation.ts
+4 -7
View File
@@ -7,13 +7,10 @@ import type { Types } from '@cornerstonejs/core';
export type PositionPresentation = {
id: string;
viewportType: string;
presentation: {
initialImageIndex: number;
viewUp: Types.Point3;
viewPlaneNormal: Types.Point3;
zoom?: number;
pan?: Types.Point2;
};
// The view reference has the basic information as to what image orientation/slice is shown
viewReference: Types.ViewReference;
// The position information has the zoom/pan and possibly other related information, but not LUT
position: Types.ViewPresentation;
};
/**
extensions/cornerstone/src/utils/getCornerstoneViewportType.ts
+19 -3
View File
@@ -1,16 +1,30 @@
import type { Types } from '@ohif/core';
import { Enums } from '@cornerstonejs/core';
const STACK = 'stack';
const VOLUME = 'volume';
const ORTHOGRAPHIC = 'orthographic';
const VOLUME_3D = 'volume3d';
const VIDEO = 'video';
const WHOLESLIDE = 'wholeslide';
export default function getCornerstoneViewportType(viewportType: string): Enums.ViewportType {
const lowerViewportType = viewportType.toLowerCase();
export default function getCornerstoneViewportType(
viewportType: string,
displaySets?: Types.DisplaySet[]
): Enums.ViewportType {
const lowerViewportType =
displaySets?.[0]?.viewportType?.toLowerCase() || viewportType.toLowerCase();
if (lowerViewportType === STACK) {
return Enums.ViewportType.STACK;
}
if (lowerViewportType === VIDEO) {
return Enums.ViewportType.VIDEO;
}
if (lowerViewportType === WHOLESLIDE) {
return Enums.ViewportType.WholeSlide;
}
if (lowerViewportType === VOLUME || lowerViewportType === ORTHOGRAPHIC) {
return Enums.ViewportType.ORTHOGRAPHIC;
}
@@ -19,5 +33,7 @@ export default function getCornerstoneViewportType(viewportType: string): Enums.
return Enums.ViewportType.VOLUME_3D;
}
throw new Error(`Invalid viewport type: ${viewportType}. Valid types are: stack, volume`);
throw new Error(
`Invalid viewport type: ${viewportType}. Valid types are: stack, volume, video, wholeslide`
);
}
extensions/cornerstone/src/utils/measurementServiceMappings/Angle.ts
+1 -1
View File
@@ -168,7 +168,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
// Area is the same for all series
const { angle, unit, SeriesNumber, SOPInstanceUID, frameNumber } = mappedAnnotations[0];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/cornerstone/src/utils/measurementServiceMappings/ArrowAnnotate.ts
+1 -1
View File
@@ -117,7 +117,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
// Area is the same for all series
const { SeriesNumber, SOPInstanceUID, frameNumber } = mappedAnnotations[0];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/cornerstone/src/utils/measurementServiceMappings/Bidirectional.ts
+1 -1
View File
@@ -165,7 +165,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
const roundedLength = utils.roundNumber(length, 2);
const roundedWidth = utils.roundNumber(width, 2);
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/cornerstone/src/utils/measurementServiceMappings/CircleROI.ts
+1 -1
View File
@@ -171,7 +171,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
// Area is the same for all series
const { area, SOPInstanceUID, frameNumber, areaUnit } = mappedAnnotations[0];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/cornerstone/src/utils/measurementServiceMappings/CobbAngle.ts
+1 -1
View File
@@ -168,7 +168,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
// Area is the same for all series
const { angle, unit, SeriesNumber, SOPInstanceUID, frameNumber } = mappedAnnotations[0];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/cornerstone/src/utils/measurementServiceMappings/EllipticalROI.ts
+1 -1
View File
@@ -171,7 +171,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
// Area is the same for all series
const { area, SOPInstanceUID, frameNumber, areaUnit } = mappedAnnotations[0];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/cornerstone/src/utils/measurementServiceMappings/Length.ts
+1 -1
View File
@@ -168,7 +168,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
// Area is the same for all series
const { length, SeriesNumber, SOPInstanceUID, frameNumber, unit } = mappedAnnotations[0];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/cornerstone/src/utils/measurementServiceMappings/LivewireContour.ts
+1 -1
View File
@@ -132,7 +132,7 @@ function getDisplayText(annotation, displaySet, customizationService) {
const displayText = [];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
InstanceNumber = instance.InstanceNumber;
extensions/cornerstone/src/utils/measurementServiceMappings/PlanarFreehandROI.ts
+1 -1
View File
@@ -139,7 +139,7 @@ function getDisplayText(annotation, displaySet, customizationService, displaySet
const displayTextArray = [];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
InstanceNumber = instance.InstanceNumber;
extensions/cornerstone/src/utils/measurementServiceMappings/Probe.ts
+1 -1
View File
@@ -163,7 +163,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
const { value, unit, SeriesNumber, SOPInstanceUID, frameNumber } = mappedAnnotations[0];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/cornerstone/src/utils/measurementServiceMappings/RectangleROI.ts
+1 -1
View File
@@ -172,7 +172,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
// Area is the same for all series
const { area, SOPInstanceUID, frameNumber, areaUnit } = mappedAnnotations[0];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/cornerstone/src/utils/measurementServiceMappings/SplineROI.ts
+1 -1
View File
@@ -138,7 +138,7 @@ function getDisplayText(annotation, displaySet, customizationService) {
const displayTextArray = [];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
InstanceNumber = instance.InstanceNumber;
extensions/cornerstone/src/utils/measurementServiceMappings/UltrasoundDirectional.ts
+1 -1
View File
@@ -176,7 +176,7 @@ function getDisplayText(mappedAnnotations, displaySet, customizationService) {
const { xValues, yValues, units, isUnitless, SeriesNumber, SOPInstanceUID, frameNumber } =
mappedAnnotations[0];
const instance = displaySet.images.find(image => image.SOPInstanceUID === SOPInstanceUID);
const instance = displaySet.instances.find(image => image.SOPInstanceUID === SOPInstanceUID);
let InstanceNumber;
if (instance) {
extensions/default/src/DicomWebDataSource/index.js
+66 -42
View File
@@ -190,6 +190,15 @@ function createDicomWebApi(dicomWebConfig, servicesManager) {
params
);
},
/**
* Provide direct access to the dicom web client for certain use cases
* where the dicom web client is used by an external library such as the
* microscopy viewer.
* Note this instance only needs to support the wado queries, and may not
* support any QIDO or STOW operations.
*/
getWadoDicomWebClient: () => wadoDicomWebClient,
bulkDataURI: async ({ StudyInstanceUID, BulkDataURI }) => {
qidoDicomWebClient.headers = getAuthrorizationHeader();
const options = {
@@ -373,6 +382,32 @@ function createDicomWebApi(dicomWebConfig, servicesManager) {
dicomWebConfig
);
/**
* Adds the retrieve bulkdata function to naturalized DICOM data.
* This is done recursively, for sub-sequences.
*/
const addRetrieveBulkDataNaturalized = (naturalized, instance = naturalized) => {
for (const key of Object.keys(naturalized)) {
const value = naturalized[key];
if (Array.isArray(value) && typeof value[0] === 'object') {
// Fix recursive values
value.forEach(child => addRetrieveBulkDataNaturalized(child, instance));
continue;
}
// The value.Value will be set with the bulkdata read value
// in which case it isn't necessary to re-read this.
if (value && value.BulkDataURI && !value.Value) {
// handle the scenarios where bulkDataURI is relative path
fixBulkDataURI(value, instance, dicomWebConfig);
// Provide a method to fetch bulkdata
value.retrieveBulkData = retrieveBulkData.bind(qidoDicomWebClient, value);
}
}
return naturalized;
};
/**
* naturalizes the dataset, and adds a retrieve bulkdata method
* to any values containing BulkDataURI.
@@ -387,48 +422,7 @@ function createDicomWebApi(dicomWebConfig, servicesManager) {
return naturalized;
}
Object.keys(naturalized).forEach(key => {
const value = naturalized[key];
// The value.Value will be set with the bulkdata read value
// in which case it isn't necessary to re-read this.
if (value && value.BulkDataURI && !value.Value) {
// handle the scenarios where bulkDataURI is relative path
fixBulkDataURI(value, naturalized, dicomWebConfig);
// Provide a method to fetch bulkdata
value.retrieveBulkData = (options = {}) => {
const { mediaType } = options;
const useOptions = {
// The bulkdata fetches work with either multipart or
// singlepart, so set multipart to false to let the server
// decide which type to respond with.
multipart: false,
BulkDataURI: value.BulkDataURI,
// The study instance UID is required if the bulkdata uri
// is relative - that isn't disallowed by DICOMweb, but
// isn't well specified in the standard, but is needed in
// any implementation that stores static copies of the metadata
StudyInstanceUID: naturalized.StudyInstanceUID,
mediaTypes: mediaType
? [{ mediaType }, { mediaType: 'application/octet-stream' }]
: undefined,
...options,
};
return qidoDicomWebClient.retrieveBulkData(useOptions).then(val => {
// 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;
});
};
}
});
return naturalized;
return addRetrieveBulkDataNaturalized(naturalized);
};
// Async load series, store as retrieved
@@ -558,4 +552,34 @@ function createDicomWebApi(dicomWebConfig, servicesManager) {
return IWebApiDataSource.create(implementation);
}
/**
* A bindable function that retrieves the bulk data against this as the
* dicomweb client, and on the given value element.
*
* @param value - a bind value that stores the retrieve value to short circuit the
* next retrieve instance.
* @param options - to allow specifying the content type.
*/
function retrieveBulkData(value, options = {}) {
const { mediaType } = options;
const useOptions = {
// The bulkdata fetches work with either multipart or
// singlepart, so set multipart to false to let the server
// decide which type to respond with.
multipart: false,
BulkDataURI: value.BulkDataURI,
mediaTypes: mediaType ? [{ mediaType }, { mediaType: 'application/octet-stream' }] : undefined,
...options,
};
return this.retrieveBulkData(useOptions).then(val => {
// 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;
});
}
export { createDicomWebApi };
extensions/default/src/DicomWebDataSource/utils/cleanDenaturalizedDataset.ts
+78
View File
@@ -0,0 +1,78 @@
import { fixBulkDataURI } from './fixBulkDataURI';
function isPrimitive(v: any) {
return !(typeof v == 'object' || Array.isArray(v));
}
const vrNumerics = new Set([
'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 function cleanDenaturalizedDataset(
obj: any,
options?: {
StudyInstanceUID: string;
SeriesInstanceUID: string;
dataSourceConfig: unknown;
}
): any {
if (Array.isArray(obj)) {
const newAry = obj.map(o => (isPrimitive(o) ? o : cleanDenaturalizedDataset(o, options)));
return newAry;
}
if (isPrimitive(obj)) {
return obj;
}
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) {
if (options?.dataSourceConfig) {
// Not needed unless data source is directly used for loading data.
fixBulkDataURI(obj[key].Value[0], options, options.dataSourceConfig);
}
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.has(obj[key].vr)) {
obj[key].Value = obj[key].Value.map(v => +v);
} else {
obj[key].Value = obj[key].Value.map(entry => cleanDenaturalizedDataset(entry, options));
}
}
});
return obj;
}
/**
* This is required to make the denaturalized data transferrable when it has
* added proxy values.
*/
export function transferDenaturalizedDataset(dataset) {
const noNull = cleanDenaturalizedDataset(dataset);
return JSON.parse(JSON.stringify(noNull));
}
extensions/default/src/DicomWebDataSource/utils/fixBulkDataURI.ts
+3 -2
View File
@@ -23,6 +23,8 @@ function fixBulkDataURI(value, instance, dicomWebConfig) {
let { BulkDataURI } = value;
const { bulkDataURI: uriConfig = {} } = dicomWebConfig;
BulkDataURI = uriConfig.transform?.(BulkDataURI) || BulkDataURI;
// Handle incorrectly prefixed origins
const { startsWith, prefixWith = '' } = uriConfig;
if (startsWith && BulkDataURI.startsWith(startsWith)) {
@@ -36,7 +38,7 @@ function fixBulkDataURI(value, instance, dicomWebConfig) {
if (
BulkDataURI.startsWith('series/') ||
BulkDataURI.startsWith('bulkdata/') ||
(uriConfig.relativeResolution === 'studies' && isInstanceStart)
(uriConfig.relativeResolution === 'studies' && !isInstanceStart)
) {
value.BulkDataURI = `${dicomWebConfig.wadoRoot}/studies/${StudyInstanceUID}/${BulkDataURI}`;
} else if (
@@ -49,7 +51,6 @@ function fixBulkDataURI(value, instance, dicomWebConfig) {
return;
}
// in case it is relative path but starts at the server (e.g., /bulk/1e, note the missing http
// in the beginning and the first character is /) There are two scenarios, whether the wado root
// is absolute or relative. In case of absolute, we need to prepend the wado root to the bulkdata
extensions/default/src/DicomWebDataSource/utils/fixMultiValueKeys.ts
+12
View File
@@ -0,0 +1,12 @@
/**
* Fix multi-valued keys so that those which are strings split by
* a backslash are returned as arrays.
*/
export function fixMultiValueKeys(naturalData, keys = ['ImageType']) {
for (const key of keys) {
if (typeof naturalData[key] === 'string') {
naturalData[key] = naturalData[key].split('\\');
}
}
return naturalData;
}
extensions/default/src/DicomWebDataSource/utils/index.ts
+7 -1
View File
@@ -1,3 +1,9 @@
import { fixBulkDataURI } from './fixBulkDataURI';
import {
cleanDenaturalizedDataset,
transferDenaturalizedDataset,
} from './cleanDenaturalizedDataset';
export { fixBulkDataURI };
export { fixMultiValueKeys } from './fixMultiValueKeys';
export { fixBulkDataURI, cleanDenaturalizedDataset, transferDenaturalizedDataset };
extensions/default/src/getSopClassHandlerModule.js
+6 -6
View File
@@ -1,12 +1,12 @@
import { isImage } from '@ohif/core/src/utils/isImage';
import sopClassDictionary from '@ohif/core/src/utils/sopClassDictionary';
import ImageSet from '@ohif/core/src/classes/ImageSet';
import isDisplaySetReconstructable from '@ohif/core/src/utils/isDisplaySetReconstructable';
import { utils, classes } from '@ohif/core';
import { id } from './id';
import getDisplaySetMessages from './getDisplaySetMessages';
import getDisplaySetsFromUnsupportedSeries from './getDisplaySetsFromUnsupportedSeries';
import { chartHandler } from './SOPClassHandlers/chartSOPClassHandler';
const { isImage, sopClassDictionary, isDisplaySetReconstructable } = utils;
const { ImageSet } = classes;
const DEFAULT_VOLUME_LOADER_SCHEME = 'cornerstoneStreamingImageVolume';
const DYNAMIC_VOLUME_LOADER_SCHEME = 'cornerstoneStreamingDynamicImageVolume';
const sopClassHandlerName = 'stack';
@@ -178,7 +178,6 @@ function getDisplaySetsFromSeries(instances) {
displaySet.setAttributes({
sopClassUids,
isClip: true,
numImageFrames: instance.NumberOfFrames,
instanceNumber: instance.InstanceNumber,
acquisitionDatetime: instance.AcquisitionDateTime,
@@ -254,7 +253,8 @@ const sopClassUids = [
sopClassDictionary.OphthalmicPhotography8BitImageStorage,
sopClassDictionary.OphthalmicPhotography16BitImageStorage,
sopClassDictionary.OphthalmicTomographyImageStorage,
sopClassDictionary.VLWholeSlideMicroscopyImageStorage,
// Handled by another sop class module
// sopClassDictionary.VLWholeSlideMicroscopyImageStorage,
sopClassDictionary.PositronEmissionTomographyImageStorage,
sopClassDictionary.EnhancedPETImageStorage,
sopClassDictionary.LegacyConvertedEnhancedPETImageStorage,
extensions/default/src/index.ts
+2
View File
@@ -17,6 +17,7 @@ import * as dicomWebUtils from './DicomWebDataSource/utils';
import { createReportDialogPrompt } from './Panels';
import createReportAsync from './Actions/createReportAsync';
import StaticWadoClient from './DicomWebDataSource/utils/StaticWadoClient';
import { cleanDenaturalizedDataset } from './DicomWebDataSource/utils';
const defaultExtension: Types.Extensions.Extension = {
/**
@@ -56,4 +57,5 @@ export {
createReportDialogPrompt,
createReportAsync,
StaticWadoClient,
cleanDenaturalizedDataset,
};
extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx
+1 -1
View File
@@ -1,12 +1,12 @@
import React, { Component } from 'react';
import PropTypes from 'prop-types';
import { LoadingIndicatorProgress } from '@ohif/ui';
import { cleanDenaturalizedDataset } from '@ohif/extension-default';
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 {
extensions/dicom-microscopy/src/index.tsx
+2 -12
View File
@@ -5,7 +5,6 @@ import getCommandsModule from './getCommandsModule';
import { Types } from '@ohif/core';
import { useViewportGrid } from '@ohif/ui';
import getDicomMicroscopySopClassHandler from './DicomMicroscopySopClassHandler';
import getDicomMicroscopySRSopClassHandler from './DicomMicroscopySRSopClassHandler';
import MicroscopyService from './services/MicroscopyService';
import { useResizeDetector } from 'react-resize-detector';
@@ -153,17 +152,8 @@ const extension: Types.Extensions.Extension = {
* 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,
}),
];
getSopClassHandlerModule(params) {
return [getDicomMicroscopySRSopClassHandler(params)];
},
getPanelModule,
extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts
-66
View File
@@ -1,66 +0,0 @@
import { dicomWebUtils } from '@ohif/extension-default';
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,
options: {
StudyInstanceUID: string;
SeriesInstanceUID: string;
dataSourceConfig: unknown;
}
): any {
if (Array.isArray(obj)) {
const newAry = obj.map(o => (isPrimitive(o) ? o : cleanDenaturalizedDataset(o, options)));
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) {
dicomWebUtils.fixBulkDataURI(obj[key].Value[0], options, options.dataSourceConfig);
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(entry => cleanDenaturalizedDataset(entry, options));
}
}
});
return obj;
}
}
extensions/dicom-video/src/getSopClassHandlerModule.js
+10 -1
View File
@@ -1,5 +1,6 @@
import { SOPClassHandlerId } from './id';
import { utils } from '@ohif/core';
import { utilities as csUtils, Enums as csEnums } from '@cornerstonejs/core';
const SOP_CLASS_UIDS = {
VIDEO_MICROSCOPIC_IMAGE_STORAGE: '1.2.840.10008.5.1.4.1.1.77.1.2.1',
@@ -50,7 +51,7 @@ const _getDisplaySetsFromSeries = (instances, servicesManager, extensionManager)
);
})
.map(instance => {
const { Modality, SOPInstanceUID, SeriesDescription = 'VIDEO' } = instance;
const { Modality, SOPInstanceUID, SeriesDescription = 'VIDEO', imageId } = instance;
const { SeriesNumber, SeriesDate, SeriesInstanceUID, StudyInstanceUID, NumberOfFrames, url } =
instance;
const videoUrl = dataSource.retrieve.directURL({
@@ -72,7 +73,10 @@ const _getDisplaySetsFromSeries = (instances, servicesManager, extensionManager)
SOPClassHandlerId,
referencedImages: null,
measurements: null,
viewportType: csEnums.ViewportType.VIDEO,
// The videoUrl is deprecated, the preferred URL is renderedUrl
videoUrl,
renderedUrl: videoUrl,
instances: [instance],
thumbnailSrc: dataSource.retrieve.directURL({
instance,
@@ -80,12 +84,17 @@ const _getDisplaySetsFromSeries = (instances, servicesManager, extensionManager)
defaultType: 'image/jpeg',
tag: 'Absent',
}),
imageIds: [imageId],
isDerivedDisplaySet: true,
isLoaded: false,
sopClassUids,
numImageFrames: NumberOfFrames,
instance,
};
csUtils.genericMetadataProvider.add(imageId, {
type: 'imageUrlModule',
metadata: { rendered: videoUrl },
});
return displaySet;
});
};
extensions/measurement-tracking/src/panels/PanelMeasurementTableTracking/index.tsx
+1 -1
View File
@@ -267,7 +267,7 @@ function _mapMeasurementToDisplay(measurement, types, displaySetService) {
const displaySets = displaySetService.getDisplaySetsForSeries(referenceSeriesUID);
if (!displaySets[0] || !displaySets[0].images) {
if (!displaySets[0]?.instances) {
throw new Error('The tracked measurements panel should only be tracking "stack" displaySets.');
}