diff --git a/extensions/cornerstone-dicom-rt/src/loadRTStruct.js b/extensions/cornerstone-dicom-rt/src/loadRTStruct.js
index 52e1bd7c7..613c2fb65 100644
--- a/extensions/cornerstone-dicom-rt/src/loadRTStruct.js
+++ b/extensions/cornerstone-dicom-rt/src/loadRTStruct.js
@@ -7,12 +7,13 @@ async function checkAndLoadContourData(instance, datasource) {
return Promise.reject('Invalid instance object or ROIContourSequence');
}
- const promises = [];
- let counter = 0;
+ const promisesMap = new Map();
for (const ROIContour of instance.ROIContourSequence) {
+ const referencedROINumber = ROIContour.ReferencedROINumber;
if (!ROIContour || !ROIContour.ContourSequence) {
- return Promise.reject('Invalid ROIContour or ContourSequence');
+ promisesMap.set(referencedROINumber, [Promise.resolve([])]);
+ continue;
}
for (const Contour of ROIContour.ContourSequence) {
@@ -21,9 +22,15 @@ async function checkAndLoadContourData(instance, datasource) {
}
const contourData = Contour.ContourData;
- counter++;
+
if (Array.isArray(contourData)) {
- promises.push(Promise.resolve(contourData));
+ promisesMap.has(referencedROINumber)
+ ? promisesMap
+ .get(referencedROINumber)
+ .push(Promise.resolve(contourData))
+ : promisesMap.set(referencedROINumber, [
+ Promise.resolve(contourData),
+ ]);
} else if (contourData && contourData.BulkDataURI) {
const bulkDataURI = contourData.BulkDataURI;
@@ -44,53 +51,59 @@ async function checkAndLoadContourData(instance, datasource) {
SOPInstanceUID: instance.SOPInstanceUID,
});
- promises.push(bulkDataPromise);
+ promisesMap.has(referencedROINumber)
+ ? promisesMap.get(referencedROINumber).push(bulkDataPromise)
+ : promisesMap.set(referencedROINumber, [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++];
+ const resolvedPromisesMap = new Map();
+ for (const [key, promiseArray] of promisesMap.entries()) {
+ resolvedPromisesMap.set(key, await Promise.allSettled(promiseArray));
+ }
- 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 = [];
+ instance.ROIContourSequence.forEach(ROIContour => {
+ try {
+ const referencedROINumber = ROIContour.ReferencedROINumber;
+ const resolvedPromises = resolvedPromisesMap.get(referencedROINumber);
- 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++;
+ if (ROIContour.ContourSequence) {
+ ROIContour.ContourSequence.forEach((Contour, index) => {
+ const promise = resolvedPromises[index];
+ if (promise.status === 'fulfilled') {
+ if (
+ Array.isArray(promise.value) &&
+ promise.value.every(Number.isFinite)
+ ) {
+ // If promise.value is already an array of numbers, use it directly
+ Contour.ContourData = promise.value;
+ } else {
+ // If the resolved promise value is a byte array (Blob), it needs to be decoded
+ const uint8Array = new Uint8Array(promise.value);
+ const textDecoder = new TextDecoder();
+ const dataUint8Array = textDecoder.decode(uint8Array);
+ if (
+ typeof dataUint8Array === 'string' &&
+ dataUint8Array.includes('\\')
+ ) {
+ Contour.ContourData = dataUint8Array
+ .split('\\')
+ .map(parseFloat);
+ } else {
+ Contour.ContourData = [];
+ }
+ }
+ } else {
+ console.error(promise.reason);
}
- Contour.ContourData = ContourData;
- } else {
- Contour.ContourData = [];
- }
- } else {
- console.error(promise.reason);
+ });
}
- });
+ } catch (error) {
+ console.error(error);
+ }
});
}
@@ -104,7 +117,7 @@ export default async function loadRTStruct(
'@ohif/extension-cornerstone.utilityModule.common'
);
const dataSource = extensionManager.getActiveDataSource()[0];
- const { useBulkDataURI } = dataSource.getConfig?.() || {};
+ const { bulkDataURI } = dataSource.getConfig?.() || {};
const { dicomLoaderService } = utilityModule.exports;
const imageIdSopInstanceUidPairs = _getImageIdSopInstanceUidPairsForDisplaySet(
@@ -116,7 +129,7 @@ export default async function loadRTStruct(
rtStructDisplaySet.isLoaded = true;
let instance = rtStructDisplaySet.instance;
- if (!useBulkDataURI) {
+ if (!bulkDataURI || !bulkDataURI.enabled) {
const segArrayBuffer = await dicomLoaderService.findDicomDataPromise(
rtStructDisplaySet,
null,
diff --git a/extensions/default/src/CustomizeableContextMenu/ContextMenuController.tsx b/extensions/default/src/CustomizableContextMenu/ContextMenuController.tsx
similarity index 100%
rename from extensions/default/src/CustomizeableContextMenu/ContextMenuController.tsx
rename to extensions/default/src/CustomizableContextMenu/ContextMenuController.tsx
diff --git a/extensions/default/src/CustomizeableContextMenu/ContextMenuItemsBuilder.test.js b/extensions/default/src/CustomizableContextMenu/ContextMenuItemsBuilder.test.js
similarity index 100%
rename from extensions/default/src/CustomizeableContextMenu/ContextMenuItemsBuilder.test.js
rename to extensions/default/src/CustomizableContextMenu/ContextMenuItemsBuilder.test.js
diff --git a/extensions/default/src/CustomizeableContextMenu/ContextMenuItemsBuilder.ts b/extensions/default/src/CustomizableContextMenu/ContextMenuItemsBuilder.ts
similarity index 100%
rename from extensions/default/src/CustomizeableContextMenu/ContextMenuItemsBuilder.ts
rename to extensions/default/src/CustomizableContextMenu/ContextMenuItemsBuilder.ts
diff --git a/extensions/default/src/CustomizeableContextMenu/defaultContextMenu.ts b/extensions/default/src/CustomizableContextMenu/defaultContextMenu.ts
similarity index 100%
rename from extensions/default/src/CustomizeableContextMenu/defaultContextMenu.ts
rename to extensions/default/src/CustomizableContextMenu/defaultContextMenu.ts
diff --git a/extensions/default/src/CustomizeableContextMenu/index.ts b/extensions/default/src/CustomizableContextMenu/index.ts
similarity index 75%
rename from extensions/default/src/CustomizeableContextMenu/index.ts
rename to extensions/default/src/CustomizableContextMenu/index.ts
index 7dc08dd3d..d0abca069 100644
--- a/extensions/default/src/CustomizeableContextMenu/index.ts
+++ b/extensions/default/src/CustomizableContextMenu/index.ts
@@ -1,11 +1,11 @@
import ContextMenuController from './ContextMenuController';
import * as ContextMenuItemsBuilder from './ContextMenuItemsBuilder';
import defaultContextMenu from './defaultContextMenu';
-import * as CustomizeableContextMenuTypes from './types';
+import * as CustomizableContextMenuTypes from './types';
export {
ContextMenuController,
- CustomizeableContextMenuTypes,
+ CustomizableContextMenuTypes,
ContextMenuItemsBuilder,
defaultContextMenu,
};
diff --git a/extensions/default/src/CustomizeableContextMenu/types.ts b/extensions/default/src/CustomizableContextMenu/types.ts
similarity index 100%
rename from extensions/default/src/CustomizeableContextMenu/types.ts
rename to extensions/default/src/CustomizableContextMenu/types.ts
diff --git a/extensions/default/src/DicomWebDataSource/index.js b/extensions/default/src/DicomWebDataSource/index.js
index 01943417e..00f82841e 100644
--- a/extensions/default/src/DicomWebDataSource/index.js
+++ b/extensions/default/src/DicomWebDataSource/index.js
@@ -24,6 +24,7 @@ import {
} from './retrieveStudyMetadata.js';
import StaticWadoClient from './utils/StaticWadoClient';
import getDirectURL from '../utils/getDirectURL';
+import { fixBulkDataURI } from './utils/fixBulkDataURI';
const { DicomMetaDictionary, DicomDict } = dcmjs.data;
@@ -373,13 +374,23 @@ function createDicomWebApi(dicomWebConfig, userAuthenticationService) {
*/
const addRetrieveBulkData = instance => {
const naturalized = naturalizeDataset(instance);
+
+ // if we konw the server doesn't use bulkDataURI, then don't
+ if (!dicomWebConfig.bulkDataURI?.enabled) {
+ 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) {
// Provide a method to fetch bulkdata
value.retrieveBulkData = () => {
+ // handle the scenarios where bulkDataURI is relative path
+ fixBulkDataURI(value, naturalized, dicomWebConfig);
+
const options = {
// The bulkdata fetches work with either multipart or
// singlepart, so set multipart to false to let the server
diff --git a/extensions/default/src/DicomWebDataSource/utils/fixBulkDataURI.ts b/extensions/default/src/DicomWebDataSource/utils/fixBulkDataURI.ts
new file mode 100644
index 000000000..1a408b597
--- /dev/null
+++ b/extensions/default/src/DicomWebDataSource/utils/fixBulkDataURI.ts
@@ -0,0 +1,56 @@
+/**
+ * Modifies a bulkDataURI to ensure it is absolute based on the DICOMWeb configuration and
+ * instance data. The modification is in-place.
+ *
+ * If the bulkDataURI is relative to the series or study (according to the DICOM standard),
+ * it is made absolute by prepending the relevant paths.
+ *
+ * In scenarios where the bulkDataURI is a server-relative path (starting with '/'), the function
+ * handles two cases:
+ *
+ * 1. If the wado root is absolute (starts with 'http'), it prepends the wado root to the bulkDataURI.
+ * 2. If the wado root is relative, no changes are needed as the bulkDataURI is already correctly relative to the server root.
+ *
+ * @param value - The object containing BulkDataURI to be fixed.
+ * @param instance - The object (DICOM instance data) containing StudyInstanceUID and SeriesInstanceUID.
+ * @param dicomWebConfig - The DICOMWeb configuration object, containing wadoRoot and potentially bulkDataURI.relativeResolution.
+ * @returns The function modifies `value` in-place, it does not return a value.
+ */
+function fixBulkDataURI(value, instance, dicomWebConfig) {
+ // in case of the relative path, make it absolute. The current DICOM standard says
+ // the bulkdataURI is relative to the series. However, there are situations where
+ // it can be relative to the study too
+ if (
+ !value.BulkDataURI.startsWith('http') &&
+ !value.BulkDataURI.startsWith('/')
+ ) {
+ if (dicomWebConfig.bulkDataURI?.relativeResolution === 'studies') {
+ value.BulkDataURI = `${dicomWebConfig.wadoRoot}/studies/${instance.StudyInstanceUID}/${value.BulkDataURI}`;
+ } else if (
+ dicomWebConfig.bulkDataURI?.relativeResolution === 'series' ||
+ !dicomWebConfig.bulkDataURI?.relativeResolution
+ ) {
+ value.BulkDataURI = `${dicomWebConfig.wadoRoot}/studies/${instance.StudyInstanceUID}/series/${instance.SeriesInstanceUID}/${value.BulkDataURI}`;
+ }
+
+ 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
+ // uri (e.g., bulkData: /bulk/1e, wado root: http://myserver.com/dicomweb, output: http://myserver.com/bulk/1e)
+ // and in case of relative wado root, we need to prepend the bulkdata uri to the wado root (e.g,. bulkData: /bulk/1e
+ // wado root: /dicomweb, output: /bulk/1e)
+ if (value.BulkDataURI[0] === '/') {
+ if (dicomWebConfig.wadoRoot.startsWith('http')) {
+ // Absolute wado root
+ const url = new URL(dicomWebConfig.wadoRoot);
+ value.BulkDataURI = `${url.origin}${value.BulkDataURI}`;
+ } else {
+ // Relative wado root, we don't need to do anything, bulkdata uri is already correct
+ }
+ }
+}
+
+export { fixBulkDataURI };
diff --git a/extensions/default/src/DicomWebDataSource/utils/index.ts b/extensions/default/src/DicomWebDataSource/utils/index.ts
new file mode 100644
index 000000000..2132253fe
--- /dev/null
+++ b/extensions/default/src/DicomWebDataSource/utils/index.ts
@@ -0,0 +1,3 @@
+import { fixBulkDataURI } from './fixBulkDataURI';
+
+export { fixBulkDataURI };
diff --git a/extensions/default/src/commandsModule.ts b/extensions/default/src/commandsModule.ts
index 230a82943..958f34b60 100644
--- a/extensions/default/src/commandsModule.ts
+++ b/extensions/default/src/commandsModule.ts
@@ -3,14 +3,14 @@ import { ServicesManager, utils, Types } from '@ohif/core';
import {
ContextMenuController,
defaultContextMenu,
-} from './CustomizeableContextMenu';
+} from './CustomizableContextMenu';
import DicomTagBrowser from './DicomTagBrowser/DicomTagBrowser';
import reuseCachedLayouts from './utils/reuseCachedLayouts';
import findViewportsByPosition, {
findOrCreateViewport as layoutFindOrCreate,
} from './findViewportsByPosition';
-import { ContextMenuProps } from './CustomizeableContextMenu/types';
+import { ContextMenuProps } from './CustomizableContextMenu/types';
import { NavigateHistory } from './types/commandModuleTypes';
import { history } from '@ohif/viewer';
diff --git a/extensions/default/src/index.ts b/extensions/default/src/index.ts
index c56f39b7e..2b023d415 100644
--- a/extensions/default/src/index.ts
+++ b/extensions/default/src/index.ts
@@ -13,8 +13,9 @@ import { id } from './id.js';
import preRegistration from './init';
import {
ContextMenuController,
- CustomizeableContextMenuTypes,
-} from './CustomizeableContextMenu';
+ CustomizableContextMenuTypes,
+} from './CustomizableContextMenu';
+import * as dicomWebUtils from './DicomWebDataSource/utils';
const defaultExtension: Types.Extensions.Extension = {
/**
@@ -47,6 +48,7 @@ export default defaultExtension;
export {
ContextMenuController,
- CustomizeableContextMenuTypes,
+ CustomizableContextMenuTypes,
getStudiesForPatientByMRN,
+ dicomWebUtils,
};
diff --git a/extensions/default/src/utils/getDirectURL.js b/extensions/default/src/utils/getDirectURL.js
index 4580b8d30..c3905e9f2 100644
--- a/extensions/default/src/utils/getDirectURL.js
+++ b/extensions/default/src/utils/getDirectURL.js
@@ -1,10 +1,4 @@
-import {
- DicomMetadataStore,
- IWebApiDataSource,
- utils,
- errorHandler,
- classes,
-} from '@ohif/core';
+import { utils } from '@ohif/core';
/**
* Generates a URL that can be used for direct retrieve of the bulkdata
@@ -57,31 +51,19 @@ const getDirectURL = (config, params) => {
const BulkDataURI =
(value && value.BulkDataURI) ||
`series/${SeriesInstanceUID}/instances/${SOPInstanceUID}${defaultPath}`;
- const hasQuery = BulkDataURI.indexOf('?') != -1;
- const hasAccept = BulkDataURI.indexOf('accept=') != -1;
+ const hasQuery = BulkDataURI.indexOf('?') !== -1;
+ const hasAccept = BulkDataURI.indexOf('accept=') !== -1;
const acceptUri =
BulkDataURI +
(hasAccept ? '' : (hasQuery ? '&' : '?') + `accept=${defaultType}`);
- if (BulkDataURI.indexOf('http') === 0) {
- if (tag === 'PixelData' || tag === 'EncapsulatedDocument') {
- return `${wadoRoot}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/instances/${SOPInstanceUID}/rendered`;
- } else {
- return acceptUri;
- }
+
+ if (tag === 'PixelData' || tag === 'EncapsulatedDocument') {
+ return `${wadoRoot}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/instances/${SOPInstanceUID}/rendered`;
}
- if (BulkDataURI.indexOf('/') === 0) {
- return wadoRoot + acceptUri;
- }
- if (BulkDataURI.indexOf('series/') == 0) {
- return `${wadoRoot}/studies/${StudyInstanceUID}/${acceptUri}`;
- }
- if (BulkDataURI.indexOf('instances/') === 0) {
- return `${wadoRoot}/studies/${StudyInstanceUID}/series/${SeriesInstanceUID}/${acceptUri}`;
- }
- if (BulkDataURI.indexOf('bulkdata/') === 0) {
- return `${wadoRoot}/studies/${StudyInstanceUID}/${acceptUri}`;
- }
- throw new Error('BulkDataURI in unknown format:' + BulkDataURI);
+
+ // The DICOMweb standard states that the default is multipart related, and then
+ // separately states that the accept parameter is the URL parameter equivalent of the accept header.
+ return acceptUri;
};
export default getDirectURL;
diff --git a/extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx b/extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx
index 4c562ece1..dc794a896 100644
--- a/extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx
+++ b/extensions/dicom-microscopy/src/DicomMicroscopyViewport.tsx
@@ -2,6 +2,7 @@ import React, { Component } from 'react';
import ReactResizeDetector from 'react-resize-detector';
import PropTypes from 'prop-types';
import debounce from 'lodash.debounce';
+import { LoadingIndicatorProgress } from '@ohif/ui';
import './DicomMicroscopyViewport.css';
import ViewportOverlay from './components/ViewportOverlay';
@@ -10,9 +11,20 @@ import dcmjs from 'dcmjs';
import cleanDenaturalizedDataset from './utils/cleanDenaturalizedDataset';
import MicroscopyService from './services/MicroscopyService';
+function transformImageTypeUnnaturalized(entry) {
+ if (entry.vr === 'CS') {
+ return {
+ vr: 'US',
+ Value: entry.Value[0].split('\\'),
+ };
+ }
+ return entry;
+}
+
class DicomMicroscopyViewport extends Component {
state = {
error: null as any,
+ isLoaded: false,
};
microscopyService: MicroscopyService;
@@ -132,6 +144,10 @@ class DicomMicroscopyViewport extends Component {
// );
// m['00200052'].Value[0] = volumeImages[0].FrameOfReferenceUID;
// }
+ // NOTE: depending on different data source, image.ImageType sometimes
+ // is a string, not a string array.
+ // m['00080008'] = transformImageTypeUnnaturalized(m['00080008']);
+
// const image = new metadataUtils.VLWholeSlideMicroscopyImage({
// metadata: m,
// });
@@ -143,8 +159,20 @@ class DicomMicroscopyViewport extends Component {
// }
metadata.forEach(m => {
+ // NOTE: depending on different data source, image.ImageType sometimes
+ // is a string, not a string array.
+ m.ImageType =
+ typeof m.ImageType === 'string'
+ ? m.ImageType.split('\\')
+ : m.ImageType;
+
const inst = cleanDenaturalizedDataset(
- dcmjs.data.DicomMetaDictionary.denaturalizeDataset(m)
+ dcmjs.data.DicomMetaDictionary.denaturalizeDataset(m),
+ {
+ StudyInstanceUID: m.StudyInstanceUID,
+ SeriesInstanceUID: m.SeriesInstanceUID,
+ dataSourceConfig: this.props.dataSource.getConfig(),
+ }
);
if (!inst['00480105']) {
// Optical Path Sequence, no OpticalPathIdentifier?
@@ -165,13 +193,7 @@ class DicomMicroscopyViewport extends Component {
metadata: inst,
});
- // NOTE: depending on different data source, image.ImageType sometimes
- // is a string, not a string array.
- const imageType =
- typeof image.ImageType === 'string'
- ? image.ImageType.split('\\')
- : image.ImageType;
- const imageFlavor = imageType[2];
+ const imageFlavor = image.ImageType[2];
if (imageFlavor === 'VOLUME' || imageFlavor === 'THUMBNAIL') {
volumeImages.push(image);
}
@@ -182,7 +204,7 @@ class DicomMicroscopyViewport extends Component {
client,
metadata: volumeImages,
retrieveRendered: false,
- controls: ['overview', 'position', 'zoom'],
+ controls: ['overview', 'position'],
};
this.viewer = new microscopyViewer(options);
@@ -237,7 +259,11 @@ class DicomMicroscopyViewport extends Component {
componentDidMount() {
const { displaySets, viewportIndex } = this.props;
const displaySet = displaySets[viewportIndex];
- this.installOpenLayersRenderer(this.container.current, displaySet);
+ this.installOpenLayersRenderer(this.container.current, displaySet).then(
+ () => {
+ this.setState({ isLoaded: true });
+ }
+ );
}
componentDidUpdate(
@@ -316,6 +342,9 @@ class DicomMicroscopyViewport extends Component {
) : (
)}
+ {this.state.isLoaded ? null : (
+
+ )}
);
}
diff --git a/extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx b/extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx
index bbe863e71..e4bb67424 100644
--- a/extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx
+++ b/extensions/dicom-microscopy/src/components/ViewportOverlay/index.tsx
@@ -1,6 +1,5 @@
import React from 'react';
import classnames from 'classnames';
-import ConfigPoint from 'config-point';
import listComponentGenerator from './listComponentGenerator';
import './ViewportOverlay.css';
@@ -11,7 +10,7 @@ import {
formatPN,
} from './utils';
-interface OverylayItem {
+interface OverlayItem {
id: string;
title: string;
value?: (props: any) => string;
@@ -28,17 +27,17 @@ interface OverylayItem {
* @returns
*/
export const generateFromConfig = ({
- topLeft,
- topRight,
- bottomLeft,
- bottomRight,
- itemGenerator,
+ topLeft = [],
+ topRight = [],
+ bottomLeft = [],
+ bottomRight = [],
+ itemGenerator = () => {},
}: {
- topLeft: OverylayItem[];
- topRight: OverylayItem[];
- bottomLeft: OverylayItem[];
- bottomRight: OverylayItem[];
- itemGenerator: (props: any) => any;
+ topLeft?: OverlayItem[];
+ topRight?: OverlayItem[];
+ bottomLeft?: OverlayItem[];
+ bottomRight?: OverlayItem[];
+ itemGenerator?: (props: any) => any;
}) => {
return (props: any) => {
const topLeftClass = 'top-viewport left-viewport text-primary-light';
@@ -127,29 +126,4 @@ const itemGenerator = (props: any) => {
);
};
-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
-);
+export default generateFromConfig({});
diff --git a/extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts b/extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts
index 91d72e3e2..49d135558 100644
--- a/extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts
+++ b/extensions/dicom-microscopy/src/utils/cleanDenaturalizedDataset.ts
@@ -1,3 +1,5 @@
+import { dicomWebUtils } from '@ohif/extension-default';
+
function isPrimitive(v: any) {
return !(typeof v == 'object' || Array.isArray(v));
}
@@ -24,10 +26,17 @@ const vrNumerics = [
* @param obj
* @returns
*/
-export default function cleanDenaturalizedDataset(obj: any): any {
+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)
+ isPrimitive(o) ? o : cleanDenaturalizedDataset(o, options)
);
return newAry;
} else if (isPrimitive(obj)) {
@@ -38,7 +47,11 @@ export default function cleanDenaturalizedDataset(obj: any): any {
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;
+ obj[key].Value[0] = dicomWebUtils.fixBulkDataURI(
+ obj[key].Value[0],
+ options,
+ options.dataSourceConfig
+ );
// prevent mixed-content blockage
if (
@@ -54,7 +67,9 @@ export default function cleanDenaturalizedDataset(obj: any): any {
} 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);
+ obj[key].Value = obj[key].Value.map(entry =>
+ cleanDenaturalizedDataset(entry, options)
+ );
}
}
});
diff --git a/extensions/dicom-microscopy/src/utils/dicomWebClient.ts b/extensions/dicom-microscopy/src/utils/dicomWebClient.ts
index 8174d6c26..bb8b1f2e7 100644
--- a/extensions/dicom-microscopy/src/utils/dicomWebClient.ts
+++ b/extensions/dicom-microscopy/src/utils/dicomWebClient.ts
@@ -1,6 +1,12 @@
import { api } from 'dicomweb-client';
import { errorHandler, DicomMetadataStore } from '@ohif/core';
+const { DICOMwebClient } = api;
+
+DICOMwebClient._buildMultipartAcceptHeaderFieldValue = () => {
+ return '*/*';
+};
+
/**
* create a DICOMwebClient object to be used by Dicom Microscopy Viewer
*
diff --git a/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx b/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx
index 99eaa6a5e..171a27bff 100644
--- a/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx
+++ b/extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/PanelStudyBrowserTracking.tsx
@@ -1,6 +1,6 @@
import React, { useState, useEffect } from 'react';
import PropTypes from 'prop-types';
-import { HangingProtocolService, utils } from '@ohif/core';
+import { utils } from '@ohif/core';
import {
StudyBrowser,
useImageViewer,
diff --git a/modes/tmtv/src/index.js b/modes/tmtv/src/index.js
index e4cfc5c25..aae993bbd 100644
--- a/modes/tmtv/src/index.js
+++ b/modes/tmtv/src/index.js
@@ -189,16 +189,26 @@ function modeFactory({ modeConfiguration }) {
study: [],
series: [],
},
- isValidMode: ({ modalities }) => {
+ isValidMode: ({ modalities, study }) => {
const modalities_list = modalities.split('\\');
const invalidModalities = ['SM'];
- // there should be both CT and PT modalities and the modality should not be SM
- return (
+ const isValid =
modalities_list.includes('CT') &&
modalities_list.includes('PT') &&
- !invalidModalities.some(modality => modalities_list.includes(modality))
- );
+ !invalidModalities.some(modality =>
+ modalities_list.includes(modality)
+ ) &&
+ // This is study is a 4D study with PT and CT and not a 3D study for the tmtv
+ // mode, until we have a better way to identify 4D studies we will use the
+ // StudyInstanceUID to identify the study
+ // Todo: when we add the 4D mode which comes with a mechanism to identify
+ // 4D studies we can use that
+ study.studyInstanceUid !==
+ '1.3.6.1.4.1.12842.1.1.14.3.20220915.105557.468.2963630849';
+
+ // there should be both CT and PT modalities and the modality should not be SM
+ return isValid;
},
routes: [
{
diff --git a/platform/docs/docs/configuration/dataSources/dicom-web.md b/platform/docs/docs/configuration/dataSources/dicom-web.md
index 2736ffc9d..24b2c16b3 100644
--- a/platform/docs/docs/configuration/dataSources/dicom-web.md
+++ b/platform/docs/docs/configuration/dataSources/dicom-web.md
@@ -179,6 +179,24 @@ See the [`singlepart`](#singlepart) data source configuration option.
### DICOM Video
See the [`singlepart`](#singlepart) data source configuration option.
+### BulkDataURI
+
+The `bulkDataURI` configuration option allows the datasource to use the
+bulkdata end points for retrieving metadata if originally was not included in the
+response from the server. This is useful for the metadata information that
+are big and can/should be retrieved in a separate request. In case the bulkData URI
+is relative (instead of absolute) the `relativeResolution` option can be used to
+specify the resolution of the relative URI. The possible values are `studies`, `series` and `instances`.
+Certainly the knowledge of how the server is configured is required to use this option.
+
+```js
+bulkDataURI: {
+ enabled: true,
+ relativeResolution: 'series',
+},
+```
+
+
### Running DCM4CHEE
dcm4che is a collection of open source applications for healthcare enterprise
diff --git a/platform/docs/docs/migration-guide.md b/platform/docs/docs/migration-guide.md
index cad1b8851..f836c8607 100644
--- a/platform/docs/docs/migration-guide.md
+++ b/platform/docs/docs/migration-guide.md
@@ -209,6 +209,13 @@ see [custom routes](./platform/services/ui/customization-service.md#customroutes
+## DICOM Endpoints
+
+In OHIF v3 there is a new end point that your DICOM server should be able to respond to
+`WADO-RS GET studies/{studyInstanceUid}/series`
+
+This is used in the viewer for fetching the series list for a study to use for the hanging protocol.
+
## LifeCycle Hooks
OHIF v2 had `preRegistration` hook for extensions for initialization. In OHIF v3 you have
diff --git a/platform/docs/docs/platform/services/ui/customization-service.md b/platform/docs/docs/platform/services/ui/customization-service.md
index b59bf10d9..516df2d24 100644
--- a/platform/docs/docs/platform/services/ui/customization-service.md
+++ b/platform/docs/docs/platform/services/ui/customization-service.md
@@ -490,7 +490,7 @@ are specific to the context used for where the menu is displayed.
The default cornerstone context menu can be customized by setting the
`cornerstoneContextMenu`. For a full example, see `findingsContextMenu`.
-## Customizeable Cornerstone Viewport Click Behaviour
+## Customizable Cornerstone Viewport Click Behaviour
The behaviour on clicking on the cornerstone viewport can be customized
by setting the `cornerstoneViewportClickCommands`. This is intended to
diff --git a/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.tsx b/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.tsx
index 2c18a8bf4..e66d1de7f 100644
--- a/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.tsx
+++ b/platform/ui/src/components/LoadingIndicatorProgress/LoadingIndicatorProgress.tsx
@@ -19,7 +19,7 @@ function LoadingIndicatorProgress({ className, textBlock, progress }) {
>
{textBlock}
diff --git a/platform/viewer/package.json b/platform/viewer/package.json
index 1f5407fa1..4a487787a 100644
--- a/platform/viewer/package.json
+++ b/platform/viewer/package.json
@@ -65,7 +65,6 @@
"@ohif/ui": "^2.0.0",
"@types/react": "^17.0.38",
"classnames": "^2.3.2",
- "config-point": "^0.4.8",
"core-js": "^3.16.1",
"cornerstone-math": "^0.1.9",
"@cornerstonejs/dicom-image-loader": "^0.6.8",
diff --git a/platform/viewer/public/config/default.js b/platform/viewer/public/config/default.js
index ff93f31a1..8ff91875b 100644
--- a/platform/viewer/public/config/default.js
+++ b/platform/viewer/public/config/default.js
@@ -48,9 +48,9 @@ window.config = {
// 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',
+ wadoUriRoot: 'https://d33do7qe4w26qo.cloudfront.net/dicomweb',
+ qidoRoot: 'https://d33do7qe4w26qo.cloudfront.net/dicomweb',
+ wadoRoot: 'https://d33do7qe4w26qo.cloudfront.net/dicomweb',
qidoSupportsIncludeField: false,
supportsReject: false,
@@ -60,8 +60,14 @@ window.config = {
supportsFuzzyMatching: false,
supportsWildcard: true,
staticWado: true,
- singlepart: 'bulkdata,video,pdf',
- useBulkDataURI: false,
+ singlepart: 'bulkdata,video',
+ // whether the data source should use retrieveBulkData to grab metadata,
+ // and in case of relative path, what would it be relative to, options
+ // are in the series level or study level (some servers like series some study)
+ bulkDataURI: {
+ enabled: true,
+ relativeResolution: 'studies',
+ },
},
},
{
diff --git a/platform/viewer/public/config/demo.js b/platform/viewer/public/config/demo.js
index 59f01cc9c..27f7bc53f 100644
--- a/platform/viewer/public/config/demo.js
+++ b/platform/viewer/public/config/demo.js
@@ -22,7 +22,9 @@ window.config = {
qidoSupportsIncludeField: true,
imageRendering: 'wadors',
enableStudyLazyLoad: true,
- useBulkDataURI: false,
+ bulkDataURI: {
+ enabled: false,
+ },
},
},
],
diff --git a/platform/viewer/public/config/local_dcm4chee.js b/platform/viewer/public/config/local_dcm4chee.js
index 682501fff..763604ffd 100644
--- a/platform/viewer/public/config/local_dcm4chee.js
+++ b/platform/viewer/public/config/local_dcm4chee.js
@@ -33,6 +33,12 @@ window.config = {
},
dicomUploadEnabled: true,
singlepart: 'pdf,video',
+ // whether the data source should use retrieveBulkData to grab metadata,
+ // and in case of relative path, what would it be relative to, options
+ // are in the series level or study level (some servers like series some study)
+ bulkDataURI: {
+ enabled: true,
+ },
},
},
{
diff --git a/platform/viewer/public/config/local_orthanc.js b/platform/viewer/public/config/local_orthanc.js
index 140f4d516..80469a291 100644
--- a/platform/viewer/public/config/local_orthanc.js
+++ b/platform/viewer/public/config/local_orthanc.js
@@ -29,10 +29,12 @@ window.config = {
imageRendering: 'wadors',
thumbnailRendering: 'wadors',
enableStudyLazyLoad: true,
- useBulkDataURI: false,
supportsFuzzyMatching: true,
supportsWildcard: true,
dicomUploadEnabled: true,
+ bulkDataURI: {
+ enabled: false,
+ },
},
},
{
diff --git a/platform/viewer/src/routes/WorkList/WorkList.tsx b/platform/viewer/src/routes/WorkList/WorkList.tsx
index df2c30376..f5c914111 100644
--- a/platform/viewer/src/routes/WorkList/WorkList.tsx
+++ b/platform/viewer/src/routes/WorkList/WorkList.tsx
@@ -343,6 +343,7 @@ function WorkList({
const isValidMode = mode.isValidMode({
modalities: modalitiesToCheck,
+ study,
});
// TODO: Modes need a default/target route? We mostly support a single one for now.
// We should also be using the route path, but currently are not
diff --git a/yarn.lock b/yarn.lock
index d414a7a5a..e0b3eea49 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1302,7 +1302,7 @@
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@^7.10.3", "@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@^7.20.6", "@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@^7.0.0", "@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@^7.17.8", "@babel/runtime@^7.18.6", "@babel/runtime@^7.20.13", "@babel/runtime@^7.20.6", "@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":
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==
@@ -7461,14 +7461,6 @@ config-chain@^1.1.11:
ini "^1.3.4"
proto-list "~1.2.1"
-config-point@^0.4.8:
- version "0.4.9"
- resolved "https://registry.npmjs.org/config-point/-/config-point-0.4.9.tgz#ec4594d04235438d5852e5ab33bde60aeffd18db"
- integrity sha512-2QyqD2eb2iURURZNW6MAcNcT2e1Pr1VXwCaMgEQM0f/i+WaUCLZOdPjFtqF7oIT1rzPXNoMfl3KK2hbNcy5dXw==
- dependencies:
- "@babel/runtime" "^7.14.6"
- json5 "^2.2.0"
-
configstore@^5.0.1:
version "5.0.1"
resolved "https://registry.npmjs.org/configstore/-/configstore-5.0.1.tgz#d365021b5df4b98cdd187d6a3b0e3f6a7cc5ed96"