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fix: retrieveSeriesMetadata (#2703)

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James Petts 2022-02-08 13:17:37 +00:00 committed by GitHub
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10 changed files with 455 additions and 443 deletions
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124
extensions/default/src/DicomJSONDataSource/index.js
View File

@ -134,8 +134,68 @@ function createDicomJSONApi(dicomJsonConfig) {
},
retrieve: {
series: {
metaData: () => {
console.debug(' DICOMJson retrieve series metadata');
metaData: ({
StudyInstanceUID,
madeInClient = false,
customSort,
} = {}) => {
if (!StudyInstanceUID) {
throw new Error(
'Unable to query for SeriesMetadata without StudyInstanceUID'
);
}
const study = findStudies('StudyInstanceUID', StudyInstanceUID)[0];
let series;
if (customSort) {
series = customSort(study.series);
} else {
series = study.series;
}
const seriesSummaryMetadata = series.map(series => {
const seriesSummary = {
StudyInstanceUID: study.StudyInstanceUID,
...series,
};
delete seriesSummary.instances;
return seriesSummary;
});
// Async load series, store as retrieved
function storeInstances(naturalizedInstances) {
DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
}
DicomMetadataStore.addSeriesMetadata(
seriesSummaryMetadata,
madeInClient
);
function setSuccessFlag() {
const study = DicomMetadataStore.getStudy(
StudyInstanceUID,
madeInClient
);
study.isLoaded = true;
}
const numberOfSeries = series.length;
series.forEach((series, index) => {
const instances = series.instances.map(instance => {
const obj = {
...instance.metadata,
url: instance.url,
imageId: instance.url,
...series,
};
delete obj.instances;
return obj;
});
storeInstances(instances);
if (index === numberOfSeries - 1) setSuccessFlag();
});
},
},
},
@ -144,66 +204,6 @@ function createDicomJSONApi(dicomJsonConfig) {
console.debug(' DICOMJson store dicom');
},
},
retrieveSeriesMetadata: ({
StudyInstanceUID,
madeInClient = false,
customSort,
} = {}) => {
if (!StudyInstanceUID) {
throw new Error(
'Unable to query for SeriesMetadata without StudyInstanceUID'
);
}
const study = findStudies('StudyInstanceUID', StudyInstanceUID)[0];
let series;
if (customSort) {
series = customSort(study.series);
} else {
series = study.series;
}
const seriesSummaryMetadata = series.map(series => {
const seriesSummary = {
StudyInstanceUID: study.StudyInstanceUID,
...series,
};
delete seriesSummary.instances;
return seriesSummary;
});
// Async load series, store as retrieved
function storeInstances(naturalizedInstances) {
DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
}
DicomMetadataStore.addSeriesMetadata(seriesSummaryMetadata, madeInClient);
function setSuccessFlag() {
const study = DicomMetadataStore.getStudy(
StudyInstanceUID,
madeInClient
);
study.isLoaded = true;
}
const numberOfSeries = series.length;
series.forEach((series, index) => {
const instances = series.instances.map(instance => {
const obj = {
...instance.metadata,
url: instance.url,
imageId: instance.url,
...series,
};
delete obj.instances;
return obj;
});
storeInstances(instances);
if (index === numberOfSeries - 1) setSuccessFlag();
});
},
getImageIdsForDisplaySet(displaySet) {
const images = displaySet.images;
const imageIds = [];

198
extensions/default/src/DicomLocalDataSource/index.js
View File

@ -1,69 +1,67 @@
import { DicomMetadataStore, IWebApiDataSource } from '@ohif/core'
import OHIF from '@ohif/core'
import { DicomMetadataStore, IWebApiDataSource } from '@ohif/core';
import OHIF from '@ohif/core';
import dcmjs from 'dcmjs';
const metadataProvider = OHIF.classes.MetadataProvider
const { EVENTS } = DicomMetadataStore
const metadataProvider = OHIF.classes.MetadataProvider;
const { EVENTS } = DicomMetadataStore;
// Sorting SR modalities to be at the end of series list
function customSort(seriesA, seriesB) {
const modalityA = seriesA.instances[0].Modality
const modalityB = seriesB.instances[0].Modality
const modalityA = seriesA.instances[0].Modality;
const modalityB = seriesB.instances[0].Modality;
if (modalityA === "SR") {
if (modalityA === 'SR') {
return +1;
}
if (modalityB === "SR") {
if (modalityB === 'SR') {
return -1;
}
return 0;
}
function createDicomLocalApi(dicomLocalConfig) {
const { name } = dicomLocalConfig
const { name } = dicomLocalConfig;
const implementation = {
initialize: ({ params, query }) => {
const { StudyInstanceUIDs: paramsStudyInstanceUIDs } = params
const queryStudyInstanceUIDs = query.get('StudyInstanceUIDs')
const { StudyInstanceUIDs: paramsStudyInstanceUIDs } = params;
const queryStudyInstanceUIDs = query.get('StudyInstanceUIDs');
const StudyInstanceUIDs =
queryStudyInstanceUIDs || paramsStudyInstanceUIDs
queryStudyInstanceUIDs || paramsStudyInstanceUIDs;
const StudyInstanceUIDsAsArray =
StudyInstanceUIDs && Array.isArray(StudyInstanceUIDs)
? StudyInstanceUIDs
: [StudyInstanceUIDs]
: [StudyInstanceUIDs];
// Put SRs at the end of series list to make sure images are loaded first
StudyInstanceUIDsAsArray.forEach(StudyInstanceUID => {
const study = DicomMetadataStore.getStudy(StudyInstanceUID)
study.series = study.series.sort(customSort)
})
const study = DicomMetadataStore.getStudy(StudyInstanceUID);
study.series = study.series.sort(customSort);
});
return StudyInstanceUIDsAsArray
return StudyInstanceUIDsAsArray;
},
query: {
studies: {
mapParams: () => { },
search: (params) => {
const studyUIDs = DicomMetadataStore.getStudyInstanceUIDs()
mapParams: () => {},
search: params => {
const studyUIDs = DicomMetadataStore.getStudyInstanceUIDs();
return studyUIDs.map(StudyInstanceUID => {
let numInstances = 0
const modalities = new Set()
let numInstances = 0;
const modalities = new Set();
// Calculating the number of instances in the study and modalities
// present in the study
const study = DicomMetadataStore.getStudy(StudyInstanceUID)
const study = DicomMetadataStore.getStudy(StudyInstanceUID);
study.series.forEach(aSeries => {
numInstances += aSeries.instances.length
numInstances += aSeries.instances.length;
modalities.add(aSeries.Modality);
})
});
// first instance in the first series
const firstInstance = study?.series[0]?.instances[0]
const firstInstance = study?.series[0]?.instances[0];
if (firstInstance) {
return {
@ -80,33 +78,75 @@ function createDicomLocalApi(dicomLocalConfig) {
NumInstances: numInstances,
};
}
})
});
},
processResults: () => {
console.debug(' DICOMLocal QUERY processResults')
console.debug(' DICOMLocal QUERY processResults');
},
},
series: {
// mapParams: mapParams.bind(),
search: () => {
console.debug(' DICOMLocal QUERY SERIES SEARCH')
console.debug(' DICOMLocal QUERY SERIES SEARCH');
},
},
instances: {
search: () => {
console.debug(' DICOMLocal QUERY instances SEARCH')
console.debug(' DICOMLocal QUERY instances SEARCH');
},
},
},
retrieve: {
series: {
metaData: () => {
console.debug(' DICOMLocal retrieve series metadata')
metaData: async ({ StudyInstanceUID, madeInClient = false } = {}) => {
if (!StudyInstanceUID) {
throw new Error(
'Unable to query for SeriesMetadata without StudyInstanceUID'
);
}
// Instances metadata already added via local upload
const study = DicomMetadataStore.getStudy(
StudyInstanceUID,
madeInClient
);
// Series metadata already added via local upload
DicomMetadataStore._broadcastEvent(EVENTS.SERIES_ADDED, {
StudyInstanceUID,
madeInClient,
});
study.series.forEach(aSeries => {
const { SeriesInstanceUID } = aSeries;
aSeries.instances.forEach(instance => {
const {
url: imageId,
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
} = instance;
// Add imageId specific mapping to this data as the URL isn't necessarily WADO-URI.
metadataProvider.addImageIdToUIDs(imageId, {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
});
});
DicomMetadataStore._broadcastEvent(EVENTS.INSTANCES_ADDED, {
StudyInstanceUID,
SeriesInstanceUID,
madeInClient,
});
});
},
},
},
store: {
dicom: (naturalizedReport) => {
dicom: naturalizedReport => {
const reportBlob = dcmjs.data.datasetToBlob(naturalizedReport);
//Create a URL for the binary.
@ -114,91 +154,49 @@ function createDicomLocalApi(dicomLocalConfig) {
window.location.assign(objectUrl);
},
},
retrieveSeriesMetadata: async ({
StudyInstanceUID,
madeInClient = false,
} = {}) => {
if (!StudyInstanceUID) {
throw new Error(
'Unable to query for SeriesMetadata without StudyInstanceUID'
)
}
// Instances metadata already added via local upload
const study = DicomMetadataStore.getStudy(StudyInstanceUID, madeInClient)
// Series metadata already added via local upload
DicomMetadataStore._broadcastEvent(EVENTS.SERIES_ADDED, {
StudyInstanceUID,
madeInClient,
})
study.series.forEach((aSeries) => {
const { SeriesInstanceUID } = aSeries
aSeries.instances.forEach((instance) => {
const {
url: imageId,
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
} = instance
// Add imageId specific mapping to this data as the URL isn't necessarily WADO-URI.
metadataProvider.addImageIdToUIDs(imageId, {
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID,
})
})
DicomMetadataStore._broadcastEvent(EVENTS.INSTANCES_ADDED, {
StudyInstanceUID,
SeriesInstanceUID,
madeInClient,
})
})
},
getImageIdsForDisplaySet(displaySet) {
const images = displaySet.images
const imageIds = []
const images = displaySet.images;
const imageIds = [];
if (!images) {
return imageIds
return imageIds;
}
displaySet.images.forEach((instance) => {
const NumberOfFrames = instance.NumberOfFrames
displaySet.images.forEach(instance => {
const NumberOfFrames = instance.NumberOfFrames;
if (NumberOfFrames > 1) {
for (let i = 0; i < NumberOfFrames; i++) {
const imageId = this.getImageIdsForInstance({
instance,
frame: i,
})
imageIds.push(imageId)
});
imageIds.push(imageId);
}
} else {
const imageId = this.getImageIdsForInstance({ instance })
imageIds.push(imageId)
const imageId = this.getImageIdsForInstance({ instance });
imageIds.push(imageId);
}
})
});
return imageIds
return imageIds;
},
getImageIdsForInstance({ instance, frame }) {
const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = instance
const storedInstance = DicomMetadataStore.getInstance(StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID)
const { StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID } = instance;
const storedInstance = DicomMetadataStore.getInstance(
StudyInstanceUID,
SeriesInstanceUID,
SOPInstanceUID
);
if (storedInstance.url) {
return storedInstance.url
return storedInstance.url;
}
},
deleteStudyMetadataPromise() {
console.log("deleteStudyMetadataPromise not implemented")
}
}
return IWebApiDataSource.create(implementation)
console.log('deleteStudyMetadataPromise not implemented');
},
};
return IWebApiDataSource.create(implementation);
}
export { createDicomLocalApi }
export { createDicomLocalApi };

233
extensions/default/src/DicomWebDataSource/index.js
View File

@ -7,7 +7,12 @@ import {
processSeriesResults,
} from './qido.js';
import dcm4cheeReject from './dcm4cheeReject';
import { DicomMetadataStore, IWebApiDataSource, utils, errorHandler } from '@ohif/core';
import {
DicomMetadataStore,
IWebApiDataSource,
utils,
errorHandler,
} from '@ohif/core';
import getImageId from './utils/getImageId';
import dcmjs from 'dcmjs';
@ -65,7 +70,9 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
// TODO -> Two clients sucks, but its better than 1000.
// TODO -> We'll need to merge auth later.
const qidoDicomWebClient = staticWado ? new StaticWadoClient(qidoConfig) : new api.DICOMwebClient(qidoConfig);
const qidoDicomWebClient = staticWado
? new StaticWadoClient(qidoConfig)
: new api.DICOMwebClient(qidoConfig);
const wadoDicomWebClient = new api.DICOMwebClient(wadoConfig);
const implementation = {
@ -84,7 +91,7 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
query: {
studies: {
mapParams: mapParams.bind(),
search: async function (origParams) {
search: async function(origParams) {
const headers = UserAuthenticationService.getAuthorizationHeader();
if (headers) {
qidoDicomWebClient.headers = headers;
@ -109,7 +116,7 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
},
series: {
// mapParams: mapParams.bind(),
search: async function (studyInstanceUid) {
search: async function(studyInstanceUid) {
const headers = UserAuthenticationService.getAuthorizationHeader();
if (headers) {
qidoDicomWebClient.headers = headers;
@ -143,48 +150,108 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
},
retrieve: {
series: {
// TODO: change queryParams to `StudyInstanceUID` for now?
// Conduct query, return a promise like others
// Await this call and add to DicomMetadataStore after receiving result
metadata: (queryParams, callback) => {
metadata: async ({
StudyInstanceUID,
filters,
sortCriteria,
sortFunction,
madeInClient = false,
} = {}) => {
const headers = UserAuthenticationService.getAuthorizationHeader();
if (headers) {
wadoDicomWebClient.headers = headers;
}
let { StudyInstanceUIDs } = urlUtil.parse(queryParams, true);
StudyInstanceUIDs = urlUtil.paramString.parseParam(StudyInstanceUIDs);
if (!StudyInstanceUIDs) {
if (!StudyInstanceUID) {
throw new Error(
'Incomplete queryParams, missing StudyInstanceUIDs'
'Unable to query for SeriesMetadata without StudyInstanceUID'
);
}
const storeInstances = instances => {
const naturalizedInstances = instances.map(naturalizeDataset);
DicomMetadataStore.addInstances(naturalizedInstances);
callback(naturalizedInstances);
};
const studyPromises = StudyInstanceUIDs.map(StudyInstanceUID =>
retrieveStudyMetadata(
wadoDicomWebClient,
StudyInstanceUID,
enableStudyLazyLoad
)
// Get Series
const {
seriesSummaryMetadata,
seriesPromises,
} = await retrieveStudyMetadata(
wadoDicomWebClient,
StudyInstanceUID,
enableStudyLazyLoad,
filters,
sortCriteria,
sortFunction
);
studyPromises.forEach(studyPromise => {
studyPromise.then(data => {
const { seriesPromises } = data;
seriesPromises.forEach(seriesPromise => {
seriesPromise.then(instances => {
storeInstances(instances);
});
});
/**
* 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);
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 = () => {
const options = {
// 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,
};
return qidoDicomWebClient
.retrieveBulkData(options)
.then(val => {
const ret = (val && val[0]) || undefined;
value.Value = ret;
return ret;
});
};
}
});
return naturalized;
};
// Async load series, store as retrieved
function storeInstances(instances) {
const naturalizedInstances = instances.map(addRetrieveBulkData);
DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
}
function setSuccessFlag() {
const study = DicomMetadataStore.getStudy(
StudyInstanceUID,
madeInClient
);
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 numberOfSeries = seriesPromises.length;
seriesPromises.forEach(async (seriesPromise, index) => {
const instances = await seriesPromise;
storeInstances(instances);
if (index === numberOfSeries - 1) setSuccessFlag();
});
},
},
@ -220,104 +287,6 @@ function createDicomWebApi(dicomWebConfig, UserAuthenticationService) {
await wadoDicomWebClient.storeInstances(options);
},
},
// TODO: Rename this it makes no sense at all
retrieveSeriesMetadata: async ({
StudyInstanceUID,
filters,
sortCriteria,
sortFunction,
madeInClient = false,
} = {}) => {
const headers = UserAuthenticationService.getAuthorizationHeader();
if (headers) {
wadoDicomWebClient.headers = headers;
}
if (!StudyInstanceUID) {
throw new Error(
'Unable to query for SeriesMetadata without StudyInstanceUID'
);
}
// Get Series
const {
seriesSummaryMetadata,
seriesPromises,
} = await retrieveStudyMetadata(
wadoDicomWebClient,
StudyInstanceUID,
enableStudyLazyLoad,
filters,
sortCriteria,
sortFunction
);
/**
* 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);
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 = () => {
const options = {
// 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,
};
return qidoDicomWebClient.retrieveBulkData(options).then(val => {
const ret = val && val[0] || undefined;
value.Value = ret;
return ret;
});
};
}
});
return naturalized
};
// Async load series, store as retrieved
function storeInstances(instances) {
const naturalizedInstances = instances.map(addRetrieveBulkData);
DicomMetadataStore.addInstances(naturalizedInstances, madeInClient);
}
function setSuccessFlag() {
const study = DicomMetadataStore.getStudy(
StudyInstanceUID,
madeInClient
);
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 numberOfSeries = seriesPromises.length;
seriesPromises.forEach(async (seriesPromise, index) => {
const instances = await seriesPromise;
storeInstances(instances);
if (index === numberOfSeries - 1) setSuccessFlag();
});
},
deleteStudyMetadataPromise,
getImageIdsForDisplaySet(displaySet) {
const images = displaySet.images;

4
extensions/default/src/Panels/requestDisplaySetCreationForStudy.js
View File

@ -2,7 +2,7 @@ function requestDisplaySetCreationForStudy(
dataSource,
DisplaySetService,
StudyInstanceUID,
madeInClient,
madeInClient
) {
// TODO: is this already short-circuited by the map of Retrieve promises?
if (
@ -13,7 +13,7 @@ function requestDisplaySetCreationForStudy(
return;
}
dataSource.retrieveSeriesMetadata({ StudyInstanceUID, madeInClient });
dataSource.retrieve.series.metadata({ StudyInstanceUID, madeInClient });
}
export default requestDisplaySetCreationForStudy;

4
extensions/measurement-tracking/src/panels/PanelStudyBrowserTracking/requestDisplaySetCreationForStudy.js
View File

@ -2,7 +2,7 @@ function requestDisplaySetCreationForStudy(
dataSource,
DisplaySetService,
StudyInstanceUID,
madeInClient,
madeInClient
) {
if (
DisplaySetService.activeDisplaySets.some(
@ -12,7 +12,7 @@ function requestDisplaySetCreationForStudy(
return;
}
dataSource.retrieveSeriesMetadata({ StudyInstanceUID, madeInClient });
dataSource.retrieve.series.metadata({ StudyInstanceUID, madeInClient });
}
export default requestDisplaySetCreationForStudy;

4
platform/core/src/DataSources/IWebApiDataSource.js
View File

@ -18,7 +18,6 @@ function create({
store,
reject,
initialize,
retrieveSeriesMetadata,
deleteStudyMetadataPromise,
getImageIdsForDisplaySet,
getImageIdsForInstance,
@ -38,7 +37,7 @@ function create({
* @param {number} params.resultsPerPage
*/
mapParams: params => params,
requestResults: () => { },
requestResults: () => {},
processResults: results => results,
},
series: {},
@ -64,7 +63,6 @@ function create({
reject: reject || defaultReject,
store: store || defaultStore,
initialize,
retrieveSeriesMetadata,
deleteStudyMetadataPromise,
getImageIdsForDisplaySet,
getImageIdsForInstance,

49
platform/docs/docs/platform/extensions/modules/data-source.md
View File

@ -2,17 +2,27 @@
sidebar_position: 3
sidebar_label: Data Source
---
# Module: Data Source
## Overview
The internal data structure of OHIF’s metadata follows naturalized DICOM JSON, A format pioneered by `dcmjs`. In short DICOM metadata headers with DICOM Keywords instead of tags and sequences as arrays, for easy development and clear code.
We have built a standard for fetching and mapping data into OHIF’s native format, which we call DataSources, and have provided one implementation of this standard.
The internal data structure of OHIF’s metadata follows naturalized DICOM JSON, A
format pioneered by `dcmjs`. In short DICOM metadata headers with DICOM Keywords
instead of tags and sequences as arrays, for easy development and clear code.
You can make another datasource implementation which communicates to your backend and maps to OHIF’s native format, then use any existing mode on your platform. Your data doesn’t even need to be DICOM if you can map some proprietary data to the correct format.
We have built a standard for fetching and mapping data into OHIF’s native
format, which we call DataSources, and have provided one implementation of this
standard.
The DataSource is also a place to add easy helper methods that platform-specific extensions can call in order to interact with the backend, meaning proprietary data interactions can be wrapped in extensions.
You can make another datasource implementation which communicates to your
backend and maps to OHIF’s native format, then use any existing mode on your
platform. Your data doesn’t even need to be DICOM if you can map some
proprietary data to the correct format.
The DataSource is also a place to add easy helper methods that platform-specific
extensions can call in order to interact with the backend, meaning proprietary
data interactions can be wrapped in extensions.
```js
const getDataSourcesModule = () => [
@ -26,13 +36,13 @@ const getDataSourcesModule = () => [
];
```
Default extension provides two main data sources that are commonly used: `dicomweb` and `dicomjson`
Default extension provides two main data sources that are commonly used:
`dicomweb` and `dicomjson`
```js
import { createDicomWebApi } from './DicomWebDataSource/index.js';
import { createDicomJSONApi } from './DicomJSONDataSource/index.js';
function getDataSourcesModule() {
return [
{
@ -49,13 +59,14 @@ function getDataSourcesModule() {
}
```
## Custom DataSource
You can add your custom datasource by creating the implementation using `IWebApiDataSource.create` from `@ohif/core`. This factory function creates a new "Web API" data source that fetches data over HTTP.
You need to make sure, you implement the following functions for the data source.
You can add your custom datasource by creating the implementation using
`IWebApiDataSource.create` from `@ohif/core`. This factory function creates a
new "Web API" data source that fetches data over HTTP.
You need to make sure, you implement the following functions for the data
source.
```js title="platform/core/src/DataSources/IWebApiDataSource.js"
function create({
@ -64,7 +75,6 @@ function create({
store,
reject,
parseRouteParams,
retrieveSeriesMetadata,
deleteStudyMetadataPromise,
getImageIdsForDisplaySet,
getImageIdsForInstance,
@ -79,15 +89,18 @@ You can take a look at `dicomweb` data source implementation to get an idea
## Static WADO Client
If the configuration for the data source has the value staticWado set, then it
is assumed that queries for the studies return a super-set of the studies, as
it is assumed to be returning a static list. The StaticWadoClient performs the
is assumed that queries for the studies return a super-set of the studies, as it
is assumed to be returning a static list. The StaticWadoClient performs the
search functionality manually, by interpretting the query parameters and then
applying them to the returned response. This functionality may be useful for
applying them to the returned response. This functionality may be useful for
other types of DICOMweb back ends, where they are capable of performing queries,
but don't allow for querying certain types of fields. However, that only works
but don't allow for querying certain types of fields. However, that only works
as long as the size of the studies list isn't too large that client side
selectiton isn't too expensive.
## DicomMetadataStore
In `OHIF-v3` we have a central location for the metadata of studies and they are located
in `DicomMetadataStore`. Your custom datasource can communicate with `DicomMetadataStore` to store, and fetch Study/Series/Instance metadata. We will learn more about `DicomMetadataStore` in services.
In `OHIF-v3` we have a central location for the metadata of studies and they are
located in `DicomMetadataStore`. Your custom datasource can communicate with
`DicomMetadataStore` to store, and fetch Study/Series/Instance metadata. We will
learn more about `DicomMetadataStore` in services.

189
platform/docs/docs/platform/modes/routes.md
View File

@ -2,22 +2,30 @@
sidebar_position: 3
sidebar_label: Routes
---
# Mode: Routes
## Overview
Modes are tied to a specific route in the viewer, and multiple modes/routes can be present within a single application. This makes `routes` config, THE most important part of the mode configuration.
Modes are tied to a specific route in the viewer, and multiple modes/routes can
be present within a single application. This makes `routes` config, THE most
important part of the mode configuration.
## Route
`@ohif/viewer` **compose** extensions to build applications on different routes for the platform.
Below, you can see a simplified version of the `longitudinal` mode and the `routes` section
which has defined one `route`. Each route has three different configuration:
`@ohif/viewer` **compose** extensions to build applications on different routes
for the platform.
- **route path**: defines the route path to access the built application for that route
- **route init**: hook that runs when application enters the defined route path, if not defined the default init function will run for the mode.
- **route layout**: defines the layout of the application for the specified route (panels, viewports)
Below, you can see a simplified version of the `longitudinal` mode and the
`routes` section which has defined one `route`. Each route has three different
configuration:
- **route path**: defines the route path to access the built application for
that route
- **route init**: hook that runs when application enters the defined route path,
if not defined the default init function will run for the mode.
- **route layout**: defines the layout of the application for the specified
route (panels, viewports)
```js
export default function mode() {
@ -56,51 +64,61 @@ export default function mode() {
},
],
},
}
};
},
},
],
/*
...
*/
}
};
}
```
### Route: path
Upon initialization the viewer will consume extensions and modes and build up the route desired, these can then be accessed via the study list, or directly via url parameters.
> Note: Currently, only one route is built for each mode, but we will enhance route
> creation to create separate routes based on the `path` config for each `route` object.
Upon initialization the viewer will consume extensions and modes and build up
the route desired, these can then be accessed via the study list, or directly
via url parameters.
> Note: Currently, only one route is built for each mode, but we will enhance
> route creation to create separate routes based on the `path` config for each
> `route` object.
There are two types of `routes` that are created by the mode.
- Routes with dataSourceName `/${mode.id}/${dataSourceName}`
- Routes without dataSourceName `/${mode.id}`
Therefore navigating to `http://localhost:3000/viewer/?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1` will run the app with the layout and functionalities of the `viewer` mode using the `defaultDataSourceName` which is defined in the [App Config](../../configuration/index.md)
You can use the same exact mode using a different registered data source (e.g., `dicomjson`) by navigating to `http://localhost:3000/viewer/dicomjson/?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1`
Therefore navigating to
`http://localhost:3000/viewer/?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1`
will run the app with the layout and functionalities of the `viewer` mode using
the `defaultDataSourceName` which is defined in the
[App Config](../../configuration/index.md)
You can use the same exact mode using a different registered data source (e.g.,
`dicomjson`) by navigating to
`http://localhost:3000/viewer/dicomjson/?StudyInstanceUIDs=1.3.6.1.4.1.25403.345050719074.3824.20170125113417.1`
### Route: init
The mode also has an init hook, which initializes the mode. If you don't define an `init`
function the `default init` function will get run (logic is located inside `Mode.jsx`). However, you
can define you own init function following certain steps which we will discuss next.
The mode also has an init hook, which initializes the mode. If you don't define
an `init` function the `default init` function will get run (logic is located
inside `Mode.jsx`). However, you can define you own init function following
certain steps which we will discuss next.
#### Default init
Default init function will:
- `retriveSeriesMetaData` for the `studyInstanceUIDs` that are defined in the URL.
- Subscribe to `instanceAdded` event, to make display sets after a series have finished
retrieving its instances metadata.
- Subscribe to `seriesAdded` event, to run the `HangingProtocolService` on the retrieves series
from the study.
- `retriveSeriesMetaData` for the `studyInstanceUIDs` that are defined in the
URL.
- Subscribe to `instanceAdded` event, to make display sets after a series have
finished retrieving its instances metadata.
- Subscribe to `seriesAdded` event, to run the `HangingProtocolService` on the
retrieves series from the study.
A *simplified* "pseudocode" for the `defaultRouteInit` is:
A _simplified_ "pseudocode" for the `defaultRouteInit` is:
```jsx
async function defaultRouteInit({
@ -108,7 +126,10 @@ async function defaultRouteInit({
studyInstanceUIDs,
dataSource,
}) {
const { DisplaySetService, HangingProtocolService } = servicesManager.services
const {
DisplaySetService,
HangingProtocolService,
} = servicesManager.services;
// subscribe to run the function after the event happens
DicomMetadataStore.subscribe(
@ -117,26 +138,26 @@ async function defaultRouteInit({
const seriesMetadata = DicomMetadataStore.getSeries(
StudyInstanceUID,
SeriesInstanceUID
)
DisplaySetService.makeDisplaySets(seriesMetadata.instances)
);
DisplaySetService.makeDisplaySets(seriesMetadata.instances);
}
)
);
studyInstanceUIDs.forEach((StudyInstanceUID) => {
dataSource.retrieveSeriesMetadata({ StudyInstanceUID })
})
studyInstanceUIDs.forEach(StudyInstanceUID => {
dataSource.retrieve.series.metadata({ StudyInstanceUID });
});
DicomMetadataStore.subscribe('seriesAdded', ({ StudyInstanceUID }) => {
const studyMetadata = DicomMetadataStore.getStudy(StudyInstanceUID)
HangingProtocolService.run(studyMetadata)
})
const studyMetadata = DicomMetadataStore.getStudy(StudyInstanceUID);
HangingProtocolService.run(studyMetadata);
});
return unsubscriptions
return unsubscriptions;
}
```
#### Writing a custom init
You can add your custom init function to enhance the default initialization for:
- Fetching annotations from a server for the current study
@ -146,11 +167,13 @@ You can add your custom init function to enhance the default initialization for:
and lots of other modifications.
You just need to make sure, the mode `retrieveSeriesMetadata`, `makeDisplaySets` and `run` the
HangingProtocols at some point. There are various `events` that you can subscribe to and add your custom logic. **point to events**
For instance for jumping to the slice where a measurement is located at the initial render, you need to follow a pattern similar to the following:
You just need to make sure, the mode `dataSource.retrieve.series.metadata`,
`makeDisplaySets` and `run` the HangingProtocols at some point. There are
various `events` that you can subscribe to and add your custom logic. **point to
events**
For instance for jumping to the slice where a measurement is located at the
initial render, you need to follow a pattern similar to the following:
```jsx
init: async ({
@ -160,64 +183,68 @@ init: async ({
dataSource,
studyInstanceUIDs,
}) => {
const { DisplaySetService } = servicesManager.services
const { DisplaySetService } = servicesManager.services;
/**
...
**/
const onDisplaySetsAdded = ({ displaySetsAdded, options }) => {
const displaySet = displaySetsAdded[0]
const { SeriesInstanceUID } = displaySet
const displaySet = displaySetsAdded[0];
const { SeriesInstanceUID } = displaySet;
const toolData = myServer.fetchMeasurements(SeriesInstanceUID)
const toolData = myServer.fetchMeasurements(SeriesInstanceUID);
if (!toolData.length) {
return
return;
}
toolData.forEach((tool) => {
toolData.forEach(tool => {
const instance = displaySet.images.find(
(image) => image.SOPInstanceUID === tool.SOPInstanceUID
)
image => image.SOPInstanceUID === tool.SOPInstanceUID
);
const { SOPInstanceUID, url } = instance
displaySet.initialImageIdIndex = displaySet.images.indexOf(instance)
})
const { SOPInstanceUID, url } = instance;
displaySet.initialImageIdIndex = displaySet.images.indexOf(instance);
});
MeasurementService.addMeasurement(/**...**/)
}
MeasurementService.addMeasurement(/**...**/);
};
// subscription to the DISPLAY_SETS_ADDED
const { unsubscribe } = DisplaySetService.subscribe(
DisplaySetService.EVENTS.DISPLAY_SETS_ADDED,
onDisplaySetsAdded
)
);
/**
...
**/
return unsubscriptions
}
return unsubscriptions;
};
```
### Route: layoutTemplate
`layoutTemplate` is the last configuration for a certain route in a `mode`. `layoutTemplate` is
a function that returns an object that configures the overall layout of the application. The returned
object has two properties:
- `id`: the id of the `layoutTemplate` being used (it should have been registered via an extension)
`layoutTemplate` is the last configuration for a certain route in a `mode`.
`layoutTemplate` is a function that returns an object that configures the
overall layout of the application. The returned object has two properties:
- `id`: the id of the `layoutTemplate` being used (it should have been
registered via an extension)
- `props`: the required properties to be passed to the `layoutTemplate`.
For instance `default extension` provides a layoutTemplate that builds the app using left/right panels
and viewports. Therefore, the `props` include `leftPanels`, `rightPanels` and `viewports` sections. Note that the `layoutTemplate` defines the properties it is expecting. So, if you write a `layoutTemplate-2` that accepts a footer section, its logic should be written in the extension, and any mode that
is interested in using `layoutTemplate-2` **should** provide the `id` for the footer component.
For instance `default extension` provides a layoutTemplate that builds the app
using left/right panels and viewports. Therefore, the `props` include
`leftPanels`, `rightPanels` and `viewports` sections. Note that the
`layoutTemplate` defines the properties it is expecting. So, if you write a
`layoutTemplate-2` that accepts a footer section, its logic should be written in
the extension, and any mode that is interested in using `layoutTemplate-2`
**should** provide the `id` for the footer component.
**What module should the footer be registered?**
```js
/*
...
@ -242,28 +269,26 @@ layoutTemplate: ({ location, servicesManager }) => {
},
],
},
}
}
};
};
/*
...
*/
```
## FAQ
> What is the difference between `onModeEnter` and `route.init`
`onModeEnter` gets run first than `route.init`; however, each route can have their own `init`, but they share the `onModeEnter`.
`onModeEnter` gets run first than `route.init`; however, each route can have
their own `init`, but they share the `onModeEnter`.
> How can I change the `workList` appearance or add a new login page?
This is where `OHIF-v3` shines! Since the default `layoutTemplate` is written for the viewer part, you can simply add a new `layoutTemplate` and use the component you have written for that route. `Mode` handle showing the correct component for the specified route.
This is where `OHIF-v3` shines! Since the default `layoutTemplate` is written
for the viewer part, you can simply add a new `layoutTemplate` and use the
component you have written for that route. `Mode` handle showing the correct
component for the specified route.
```js
export default function mode() {
@ -278,15 +303,15 @@ export default function mode() {
return {
id: 'worklistLayout',
props: {
component: 'myNewWorkList'
component: 'myNewWorkList',
},
}
};
},
},
],
/*
...
*/
}
};
}
```

85
platform/docs/docs/platform/services/pubsub.md
View File

@ -2,20 +2,25 @@
sidebar_position: 4
sidebar_label: Pub Sub
---
# Pub sub
## Overview
Publish–subscribe pattern is a messaging pattern that is one of the fundamentals patterns used in reusable software components.
In short, services that implements this pattern, can have listeners subscribed to their broadcasted events. After the event is fired, the corresponding listener will execute the function that is registered.
Publish–subscribe pattern is a messaging pattern that is one of the fundamentals
patterns used in reusable software components.
You can read more about this design pattern [here](https://cloud.google.com/pubsub/docs/overview).
In short, services that implements this pattern, can have listeners subscribed
to their broadcasted events. After the event is fired, the corresponding
listener will execute the function that is registered.
You can read more about this design pattern
[here](https://cloud.google.com/pubsub/docs/overview).
## Example: Default Initialization
In `Mode.jsx` we have a default initialization that demonstrates
a series of subscriptions to various events.
In `Mode.jsx` we have a default initialization that demonstrates a series of
subscriptions to various events.
```js
async function defaultRouteInit({
@ -47,7 +52,7 @@ async function defaultRouteInit({
unsubscriptions.push(instanceAddedUnsubscribe);
studyInstanceUIDs.forEach(StudyInstanceUID => {
dataSource.retrieveSeriesMetadata({ StudyInstanceUID });
dataSource.retrieve.series.metadata({ StudyInstanceUID });
});
const { unsubscribe: seriesAddedUnsubscribe } = DicomMetadataStore.subscribe(
@ -64,50 +69,52 @@ async function defaultRouteInit({
```
## Unsubscription
You need to be careful if you are adding custom subscriptions to the app. Each subscription will return a unsubscription function that needs to be executed on component destruction to avoid adding multiple subscriptions to the same observer.
Below, we can see `simplified` `Mode.jsx` and the corresponding `useEffect` where the unsubscription functions are executed upon destruction.
You need to be careful if you are adding custom subscriptions to the app. Each
subscription will return a unsubscription function that needs to be executed on
component destruction to avoid adding multiple subscriptions to the same
observer.
Below, we can see `simplified` `Mode.jsx` and the corresponding `useEffect`
where the unsubscription functions are executed upon destruction.
```js title="platform/viewer/src/routes/Mode/Mode.jsx"
export default function ModeRoute(/**..**/) {
/**...**/
useEffect(
() => {
/**...**/
useEffect(() => {
/**...**/
DisplaySetService.init(extensionManager, sopClassHandlers)
DisplaySetService.init(extensionManager, sopClassHandlers);
extensionManager.onModeEnter()
mode?.onModeEnter({ servicesManager, extensionManager })
extensionManager.onModeEnter();
mode?.onModeEnter({ servicesManager, extensionManager });
hangingProtocols.forEach((extentionProtocols) => {
const { protocols } =
extensionManager.getModuleEntry(extentionProtocols)
HangingProtocolService.addProtocols(protocols)
})
hangingProtocols.forEach(extentionProtocols => {
const { protocols } = extensionManager.getModuleEntry(extentionProtocols);
HangingProtocolService.addProtocols(protocols);
});
const setupRouteInit = async () => {
if (route.init) {
return await route.init(/**...**/)
}
return await defaultRouteInit(/**...**/)
const setupRouteInit = async () => {
if (route.init) {
return await route.init(/**...**/);
}
let unsubscriptions
setupRouteInit().then((unsubs) => {
unsubscriptions = unsubs
})
return await defaultRouteInit(/**...**/);
};
return () => {
extensionManager.onModeExit()
mode?.onModeExit({ servicesManager, extensionManager })
unsubscriptions.forEach((unsub) => {
unsub()
})
}
},
)
return <> /**...**/ </>
let unsubscriptions;
setupRouteInit().then(unsubs => {
unsubscriptions = unsubs;
});
return () => {
extensionManager.onModeExit();
mode?.onModeExit({ servicesManager, extensionManager });
unsubscriptions.forEach(unsub => {
unsub();
});
};
});
return <> /**...**/ </>;
}
```

8
platform/viewer/src/routes/Mode/Mode.jsx
View File

@ -49,7 +49,7 @@ async function defaultRouteInit({
unsubscriptions.push(seriesAddedUnsubscribe);
studyInstanceUIDs.forEach(StudyInstanceUID => {
dataSource.retrieveSeriesMetadata({ StudyInstanceUID });
dataSource.retrieve.series.metadata({ StudyInstanceUID });
});
return unsubscriptions;
@ -216,7 +216,9 @@ export default function ModeRoute({
// Adding hanging protocols of extensions after onModeEnter since
// it will reset the protocols
hangingProtocols.forEach(extentionProtocols => {
const hangingProtocolModule = extensionManager.getModuleEntry(extentionProtocols);
const hangingProtocolModule = extensionManager.getModuleEntry(
extentionProtocols
);
if (hangingProtocolModule?.protocols) {
HangingProtocolService.addProtocols(hangingProtocolModule.protocols);
}
@ -280,7 +282,7 @@ export default function ModeRoute({
<ImageViewerProvider
// initialState={{ StudyInstanceUIDs: StudyInstanceUIDs }}
StudyInstanceUIDs={studyInstanceUIDs}
// reducer={reducer}
// reducer={reducer}
>
<CombinedContextProvider>
<DragAndDropProvider>