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import { DicomMetadataStore, IWebApiDataSource, utils, errorHandler, classes } from '@ohif/core';
import {
mapParams,
search as qidoSearch,
seriesInStudy,
processResults,
processSeriesResults,
} from './qido.js';
import dcm4cheeReject from './dcm4cheeReject.js';
import getImageId from './utils/getImageId.js';
import dcmjs from 'dcmjs';
import { retrieveStudyMetadata, deleteStudyMetadataPromise } from './retrieveStudyMetadata.js';
import StaticWadoClient from './utils/StaticWadoClient';
import getDirectURL from '../utils/getDirectURL';
import { fixBulkDataURI } from './utils/fixBulkDataURI';
const { DicomMetaDictionary, DicomDict } = dcmjs.data;
const { naturalizeDataset, denaturalizeDataset } = DicomMetaDictionary;
const ImplementationClassUID = '2.25.270695996825855179949881587723571202391.2.0.0';
const ImplementationVersionName = 'OHIF-VIEWER-2.0.0';
const EXPLICIT_VR_LITTLE_ENDIAN = '1.2.840.10008.1.2.1';
const metadataProvider = classes.MetadataProvider;
export type DicomWebConfig = {
/** Data source name */
name: string;
// wadoUriRoot - Legacy? (potentially unused/replaced)
/** Base URL to use for QIDO requests */
qidoRoot?: string;
wadoRoot?: string; // - Base URL to use for WADO requests
wadoUri?: string; // - Base URL to use for WADO URI requests
qidoSupportsIncludeField?: boolean; // - Whether QIDO supports the "Include" option to request additional fields in response
imageRendering?: string; // - wadors | ? (unsure of where/how this is used)
thumbnailRendering?: string; // - wadors | ? (unsure of where/how this is used)
/** Whether the server supports reject calls (i.e. DCM4CHEE) */
supportsReject?: boolean;
/** Request series meta async instead of blocking */
lazyLoadStudy?: boolean;
/** indicates if the retrieves can fetch singlepart. Options are bulkdata, video, image, or true */
singlepart?: boolean | string;
/** Transfer syntax to request from the server */
requestTransferSyntaxUID?: string;
acceptHeader?: string[]; // - Accept header to use for requests
/** Whether to omit quotation marks for multipart requests */
omitQuotationForMultipartRequest?: boolean;
/** Whether the server supports fuzzy matching */
supportsFuzzyMatching?: boolean;
/** Whether the server supports wildcard matching */
supportsWildcard?: boolean;
/** Whether the server supports the native DICOM model */
supportsNativeDICOMModel?: boolean;
/** Whether to enable request tag */
enableRequestTag?: boolean;
/** Whether to enable study lazy loading */
enableStudyLazyLoad?: boolean;
/** Whether to enable bulkDataURI */
bulkDataURI?: BulkDataURIConfig;
/** Function that is called after the configuration is initialized */
onConfiguration: (config: DicomWebConfig, params) => DicomWebConfig;
/** Whether to use the static WADO client */
staticWado?: boolean;
/** User authentication service */
userAuthenticationService: Record<string, unknown>;
};
export type BulkDataURIConfig = {
/** Enable bulkdata uri configuration */
enabled?: boolean;
/**
* Remove the startsWith string.
* This is used to correct reverse proxied URLs by removing the startsWith path
*/
startsWith?: string;
/**
* Adds this prefix path. Only used if the startsWith is defined and has
* been removed. This allows replacing the base path.
*/
prefixWith?: string;
/** Transform the bulkdata path. Used to replace a portion of the path */
transform?: (uri: string) => string;
/**
* Adds relative resolution to the path handling.
* series is the default, as the metadata retrieved is series level.
*/
relativeResolution?: 'studies' | 'series';
};
/**
* Creates a DICOM Web API based on the provided configuration.
*
* @param dicomWebConfig - Configuration for the DICOM Web API
* @returns DICOM Web API object
*/
function createDicomWebApi(dicomWebConfig: DicomWebConfig, servicesManager) {
const { userAuthenticationService } = servicesManager.services;
let dicomWebConfigCopy,
qidoConfig,
wadoConfig,
qidoDicomWebClient,
wadoDicomWebClient,
getAuthorizationHeader,
generateWadoHeader;
// Default to enabling bulk data retrieves, with no other customization as
// this is part of hte base standard.
dicomWebConfig.bulkDataURI ||= { enabled: true };
const implementation = {
initialize: ({ params, query }) => {
Iif (dicomWebConfig.onConfiguration && typeof dicomWebConfig.onConfiguration === 'function') {
dicomWebConfig = dicomWebConfig.onConfiguration(dicomWebConfig, {
params,
query,
});
}
dicomWebConfigCopy = JSON.parse(JSON.stringify(dicomWebConfig));
getAuthorizationHeader = () => {
const xhrRequestHeaders = {};
const authHeaders = userAuthenticationService.getAuthorizationHeader();
Iif (authHeaders && authHeaders.Authorization) {
xhrRequestHeaders.Authorization = authHeaders.Authorization;
}
return xhrRequestHeaders;
};
generateWadoHeader = () => {
const authorizationHeader = getAuthorizationHeader();
//Generate accept header depending on config params
const formattedAcceptHeader = utils.generateAcceptHeader(
dicomWebConfig.acceptHeader,
dicomWebConfig.requestTransferSyntaxUID,
dicomWebConfig.omitQuotationForMultipartRequest
);
return {
...authorizationHeader,
Accept: formattedAcceptHeader,
};
};
qidoConfig = {
url: dicomWebConfig.qidoRoot,
staticWado: dicomWebConfig.staticWado,
singlepart: dicomWebConfig.singlepart,
headers: userAuthenticationService.getAuthorizationHeader(),
errorInterceptor: errorHandler.getHTTPErrorHandler(),
supportsFuzzyMatching: dicomWebConfig.supportsFuzzyMatching,
};
wadoConfig = {
url: dicomWebConfig.wadoRoot,
staticWado: dicomWebConfig.staticWado,
singlepart: dicomWebConfig.singlepart,
headers: userAuthenticationService.getAuthorizationHeader(),
errorInterceptor: errorHandler.getHTTPErrorHandler(),
supportsFuzzyMatching: dicomWebConfig.supportsFuzzyMatching,
};
// TODO -> Two clients sucks, but its better than 1000.
// TODO -> We'll need to merge auth later.
qidoDicomWebClient = dicomWebConfig.staticWado
? new StaticWadoClient(qidoConfig)
: new api.DICOMwebClient(qidoConfig);
wadoDicomWebClient = dicomWebConfig.staticWado
? new StaticWadoClient(wadoConfig)
: new api.DICOMwebClient(wadoConfig);
},
query: {
studies: {
mapParams: mapParams.bind(),
search: async function (origParams) {
qidoDicomWebClient.headers = getAuthorizationHeader();
const { studyInstanceUid, seriesInstanceUid, ...mappedParams } =
mapParams(origParams, {
supportsFuzzyMatching: dicomWebConfig.supportsFuzzyMatching,
supportsWildcard: dicomWebConfig.supportsWildcard,
}) || {};
const results = await qidoSearch(qidoDicomWebClient, undefined, undefined, mappedParams);
return processResults(results);
},
processResults: processResults.bind(),
},
series: {
// mapParams: mapParams.bind(),
search: async function (studyInstanceUid) {
qidoDicomWebClient.headers = getAuthorizationHeader();
const results = await seriesInStudy(qidoDicomWebClient, studyInstanceUid);
return processSeriesResults(results);
},
// processResults: processResults.bind(),
},
instances: {
search: (studyInstanceUid, queryParameters) => {
qidoDicomWebClient.headers = getAuthorizationHeader();
return qidoSearch.call(
undefined,
qidoDicomWebClient,
studyInstanceUid,
null,
queryParameters
);
},
},
},
retrieve: {
/**
* Generates a URL that can be used for direct retrieve of the bulkdata
*
* @param {object} params
* @param {string} params.tag is the tag name of the URL to retrieve
* @param {object} params.instance is the instance object that the tag is in
* @param {string} params.defaultType is the mime type of the response
* @param {string} params.singlepart is the type of the part to retrieve
* @returns an absolute URL to the resource, if the absolute URL can be retrieved as singlepart,
* or is already retrieved, or a promise to a URL for such use if a BulkDataURI
*/
directURL: params => {
return getDirectURL(
{
wadoRoot: dicomWebConfig.wadoRoot,
singlepart: dicomWebConfig.singlepart,
},
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 = getAuthorizationHeader();
const options = {
multipart: false,
BulkDataURI,
StudyInstanceUID,
};
return qidoDicomWebClient.retrieveBulkData(options).then(val => {
const ret = (val && val[0]) || undefined;
return ret;
});
},
series: {
metadata: async ({
StudyInstanceUID,
filters,
sortCriteria,
sortFunction,
madeInClient = false,
returnPromises = false,
} = {}) => {
Iif (!StudyInstanceUID) {
throw new Error('Unable to query for SeriesMetadata without StudyInstanceUID');
}
if (dicomWebConfig.enableStudyLazyLoad) {
return implementation._retrieveSeriesMetadataAsync(
StudyInstanceUID,
filters,
sortCriteria,
sortFunction,
madeInClient,
returnPromises
);
}
return implementation._retrieveSeriesMetadataSync(
StudyInstanceUID,
filters,
sortCriteria,
sortFunction,
madeInClient
);
},
},
},
store: {
dicom: async (dataset, request, dicomDict) => {
wadoDicomWebClient.headers = getAuthorizationHeader();
if (dataset instanceof ArrayBuffer) {
const options = {
datasets: [dataset],
request,
};
await wadoDicomWebClient.storeInstances(options);
} else {
let effectiveDicomDict = dicomDict;
Iif (!dicomDict) {
const meta = {
FileMetaInformationVersion: dataset._meta?.FileMetaInformationVersion?.Value,
MediaStorageSOPClassUID: dataset.SOPClassUID,
MediaStorageSOPInstanceUID: dataset.SOPInstanceUID,
TransferSyntaxUID: EXPLICIT_VR_LITTLE_ENDIAN,
ImplementationClassUID,
ImplementationVersionName,
};
const denaturalized = denaturalizeDataset(meta);
const defaultDicomDict = new DicomDict(denaturalized);
defaultDicomDict.dict = denaturalizeDataset(dataset);
effectiveDicomDict = defaultDicomDict;
}
const part10Buffer = effectiveDicomDict.write();
const options = {
datasets: [part10Buffer],
request,
};
await wadoDicomWebClient.storeInstances(options);
}
},
},
_retrieveSeriesMetadataSync: async (
StudyInstanceUID,
filters,
sortCriteria,
sortFunction,
madeInClient
) => {
const enableStudyLazyLoad = false;
wadoDicomWebClient.headers = generateWadoHeader();
// data is all SOPInstanceUIDs
const data = await retrieveStudyMetadata(
wadoDicomWebClient,
StudyInstanceUID,
enableStudyLazyLoad,
filters,
sortCriteria,
sortFunction,
dicomWebConfig
);
// first naturalize the data
const naturalizedInstancesMetadata = data.map(naturalizeDataset);
const seriesSummaryMetadata = {};
const instancesPerSeries = {};
naturalizedInstancesMetadata.forEach(instance => {
Iif (!seriesSummaryMetadata[instance.SeriesInstanceUID]) {
seriesSummaryMetadata[instance.SeriesInstanceUID] = {
StudyInstanceUID: instance.StudyInstanceUID,
StudyDescription: instance.StudyDescription,
SeriesInstanceUID: instance.SeriesInstanceUID,
SeriesDescription: instance.SeriesDescription,
SeriesNumber: instance.SeriesNumber,
SeriesTime: instance.SeriesTime,
SOPClassUID: instance.SOPClassUID,
ProtocolName: instance.ProtocolName,
Modality: instance.Modality,
};
}
Iif (!instancesPerSeries[instance.SeriesInstanceUID]) {
instancesPerSeries[instance.SeriesInstanceUID] = [];
}
const imageId = implementation.getImageIdsForInstance({
instance,
});
instance.imageId = imageId;
instance.wadoRoot = dicomWebConfig.wadoRoot;
instance.wadoUri = dicomWebConfig.wadoUri;
metadataProvider.addImageIdToUIDs(imageId, {
StudyInstanceUID,
SeriesInstanceUID: instance.SeriesInstanceUID,
SOPInstanceUID: instance.SOPInstanceUID,
});
instancesPerSeries[instance.SeriesInstanceUID].push(instance);
});
// grab all the series metadata
const seriesMetadata = Object.values(seriesSummaryMetadata);
DicomMetadataStore.addSeriesMetadata(seriesMetadata, madeInClient);
Object.keys(instancesPerSeries).forEach(seriesInstanceUID =>
DicomMetadataStore.addInstances(instancesPerSeries[seriesInstanceUID], madeInClient)
);
return seriesSummaryMetadata;
},
_retrieveSeriesMetadataAsync: async (
StudyInstanceUID,
filters,
sortCriteria,
sortFunction,
madeInClient = false,
returnPromises = false
) => {
const enableStudyLazyLoad = true;
wadoDicomWebClient.headers = generateWadoHeader();
// Get Series
const { preLoadData: seriesSummaryMetadata, promises: seriesPromises } =
await retrieveStudyMetadata(
wadoDicomWebClient,
StudyInstanceUID,
enableStudyLazyLoad,
filters,
sortCriteria,
sortFunction,
dicomWebConfig
);
/**
* Adds the retrieve bulkdata function to naturalized DICOM data.
* This is done recursively, for sub-sequences.
*/
const addRetrieveBulkDataNaturalized = (naturalized, instance = naturalized) => {
Iif (!naturalized) {
return naturalized;
}
for (const key of Object.keys(naturalized)) {
const value = naturalized[key];
if (Array.isArray(value) && typeof value[0] === 'object') {
// Fix recursive values
const validValues = value.filter(Boolean);
validValues.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.
* @param {*} instance
* @returns naturalized dataset, with retrieveBulkData methods
*/
const addRetrieveBulkData = instance => {
const naturalized = naturalizeDataset(instance);
// if we know the server doesn't use bulkDataURI, then don't
Iif (!dicomWebConfig.bulkDataURI?.enabled) {
return naturalized;
}
return addRetrieveBulkDataNaturalized(naturalized);
};
// Async load series, store as retrieved
function storeInstances(instances) {
const naturalizedInstances = instances.map(addRetrieveBulkData);
// Adding instanceMetadata to OHIF MetadataProvider
naturalizedInstances.forEach(instance => {
instance.wadoRoot = dicomWebConfig.wadoRoot;
instance.wadoUri = dicomWebConfig.wadoUri;
const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = instance;
const numberOfFrames = instance.NumberOfFrames || 1;
// Process all frames consistently, whether single or multiframe
for (let i = 0; i < numberOfFrames; i++) {
const frameNumber = i + 1;
const frameImageId = implementation.getImageIdsForInstance({
instance,
frame: frameNumber,
});
// Add imageId specific mapping to this data as the URL isn't necessarily WADO-URI.
metadataProvider.addImageIdToUIDs(frameImageId, {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
frameNumber: numberOfFrames > 1 ? frameNumber : undefined,
});
}
// Adding imageId to each instance
// Todo: This is not the best way I can think of to let external
// metadata handlers know about the imageId that is stored in the store
const imageId = implementation.getImageIdsForInstance({
instance,
});
instance.imageId = imageId;
});
DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
}
function setSuccessFlag() {
const study = DicomMetadataStore.getStudy(StudyInstanceUID);
Iif (!study) {
return;
}
study.isLoaded = true;
}
// Google Cloud Healthcare doesn't return StudyInstanceUID, so we need to add
// it manually here
seriesSummaryMetadata.forEach(aSeries => {
aSeries.StudyInstanceUID = StudyInstanceUID;
});
DicomMetadataStore.addSeriesMetadata(seriesSummaryMetadata, madeInClient);
const seriesDeliveredPromises = seriesPromises.map(promise => {
Iif (!returnPromises) {
promise?.start();
}
return promise.then(instances => {
storeInstances(instances);
});
});
if (returnPromises) {
Promise.all(seriesDeliveredPromises).then(() => setSuccessFlag());
return seriesPromises;
} else E{
await Promise.all(seriesDeliveredPromises);
setSuccessFlag();
}
return seriesSummaryMetadata;
},
deleteStudyMetadataPromise,
getImageIdsForDisplaySet(displaySet) {
const images = displaySet.images;
const imageIds = [];
if (!images) {
return imageIds;
}
displaySet.images.forEach(instance => {
const NumberOfFrames = instance.NumberOfFrames;
Iif (NumberOfFrames > 1) {
for (let frame = 1; frame <= NumberOfFrames; frame++) {
const imageId = this.getImageIdsForInstance({
instance,
frame,
});
imageIds.push(imageId);
}
} else {
const imageId = this.getImageIdsForInstance({ instance });
imageIds.push(imageId);
}
});
return imageIds;
},
getImageIdsForInstance({ instance, frame = undefined }) {
const imageIds = getImageId({
instance,
frame,
config: dicomWebConfig,
});
return imageIds;
},
getConfig() {
return dicomWebConfigCopy;
},
getStudyInstanceUIDs({ params, query }) {
const paramsStudyInstanceUIDs = params.StudyInstanceUIDs || params.studyInstanceUIDs;
const queryStudyInstanceUIDs = utils.splitComma(
query.getAll('StudyInstanceUIDs').concat(query.getAll('studyInstanceUIDs'))
);
const StudyInstanceUIDs =
(queryStudyInstanceUIDs.length && queryStudyInstanceUIDs) || paramsStudyInstanceUIDs;
const StudyInstanceUIDsAsArray =
StudyInstanceUIDs && Array.isArray(StudyInstanceUIDs)
? StudyInstanceUIDs
: [StudyInstanceUIDs];
return StudyInstanceUIDsAsArray;
},
};
if (dicomWebConfig.supportsReject) {
implementation.reject = dcm4cheeReject(dicomWebConfig.wadoRoot, getAuthorizationHeader);
}
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 };
|