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feat: 🎸 DICOM SR STOW on MeasurementAPI (#954)

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* feat: 🎸 DICOM SR STOW on MeasurementAPI

Closes: #758

* feat: 🎸 Adding the dataExchance from DICOM SR

* feat: 🎸 Fix some issues and get the retrieve measurements working

* feat: 🎸 Preventing measurement tool helpers to broke because the data is not Number (it comes as string from dcmjs)

* feat: 🎸 Adding a button to start testing SATE functionality

* feat: 🎸Small fixes into the code

* feat: 🎸 MAke sure we get latest SR in the study, even on lazyLoad mode

* Revert "feat: 🎸 Preventing measurement tool helpers to broke because the data is not Number (it comes as string from dcmjs)"

This reverts commit 4b3a1efb5810487d2319826fd59c03d779882b5e.

* feat: 🎸 Make sure after sync we update the viewports and also that annotation tools are set to passive, so it can be drawn in the viewports

* feat: 🎸 Remove console logs and start using OHIF.log

* feat: 🎸 Refactor measurement table to use Snackbar service of messages and make sure we only show save button if server type is dicomWeb

* feat: 🎸 Refactor to remove mocked wadoRoot and use server

* Fix to expose error once we can't save the SR

* Update DCMJS into latest dev version

* Update dcmjs with latest fixes

* Fix PR callouts

* Logging error on MeasurementReport creation

* Preventing from breaking on non supported tools and also warning that some toolType is not sopported

* Small error message update

* Expose better the errors and when we have unsopported tools into the measurements

* Renaming variable

* Expose dcmjs tool support check

* Change the way we warn the unsupportedTools

* Adding style to the button

* Small change on button style

* Fix git conflicts

* Fix after merge with latest master

* Fix after merge with master, btn was not clickable

* Fixing callouts

* Adding util functions into files and refactor with JSDocs

* Refactoring code, adding some basic JSDocs

* Bump dcmjs with latest version and fixes

* JSDocs and small refactors

* yarn lock file after dcmjs update

* Remove unused parameters

* Registering a plain copy of server into measurementAPI

* Small refactor

* Start changing from toolType to toolName

* Rename a function to get instanceMetadata

* Adding error if server is not DICOMWeb on retrieve

* Move snackbar outside of UI component and use UINotificationService

* Refactor and JSDocs

* Small fixes on JSDocs (style)

* Remove unused import

* Improve JSDocs on MeasurementApi

* Remove refactor leftover

* Improve JSDocs and propTypes

* JSDocs and small refactors
This commit is contained in:
Gustavo André Lelis 2019-12-11 13:14:01 -03:00 committed by Danny Brown
parent 5cda5159da
commit ebe1af8d4f
25 changed files with 772 additions and 133 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
extensions/cornerstone/package.json
View File

@ -34,7 +34,7 @@
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "^4.8.0",
"cornerstone-wado-image-loader": "^3.0.0",
"dcmjs": "^0.6.1",
"dcmjs": "^0.8.2",
"dicom-parser": "^1.8.3",
"hammerjs": "^2.0.8",
"prop-types": "^15.6.2",

10
extensions/cornerstone/src/init.js
View File

@ -123,6 +123,16 @@ export default function init({ servicesManager, configuration }) {
csTools.addTool(tool, props);
});
// TODO -> We need a better way to do this with maybe global tool state setting all tools passive.
const BaseAnnotationTool = csTools.importInternal('base/BaseAnnotationTool');
tools.forEach(tool => {
if (tool.prototype instanceof BaseAnnotationTool) {
// BaseAnnotationTool would likely come from csTools lib exports
const toolName = new tool().name;
csTools.setToolPassive(toolName); // there may be a better place to determine name; may not be on uninstantiated class
}
});
csTools.setToolActive('Pan', { mouseButtonMask: 4 });
csTools.setToolActive('Zoom', { mouseButtonMask: 2 });
csTools.setToolActive('Wwwc', { mouseButtonMask: 1 });

2
extensions/dicom-html/package.json
View File

@ -29,7 +29,7 @@
},
"peerDependencies": {
"@ohif/core": "^0.50.0",
"dcmjs": "^0.6.1",
"dcmjs": "^0.8.2",
"prop-types": "^15.6.2",
"react": "^16.8.6",
"react-dom": "^16.8.6"

3
extensions/vtk/package.json
View File

@ -34,7 +34,7 @@
"@ohif/ui": "^0.50.0",
"cornerstone-core": "^2.2.8",
"cornerstone-wado-image-loader": "^3.0.0",
"dcmjs": "^0.6.1",
"dcmjs": "^0.8.2",
"dicom-parser": "^1.8.3",
"i18next": "^17.0.3",
"i18next-browser-languagedetector": "^3.0.1",
@ -56,7 +56,6 @@
"@ohif/ui": "^1.0.1",
"cornerstone-tools": "^4.8.0",
"cornerstone-wado-image-loader": "^3.0.0",
"dcmjs": "^0.6.1",
"dicom-parser": "^1.8.3",
"gh-pages": "^2.0.1",
"i18next": "^17.0.3",

33
platform/core/src/measurements/classes/MeasurementApi.js
View File

@ -1,4 +1,5 @@
import cornerstoneTools from 'cornerstone-tools';
import cornerstone from 'cornerstone-core';
import log from '../../log';
import getLabel from '../lib/getLabel';
import getDescription from '../lib/getDescription';
@ -7,13 +8,32 @@ import guid from '../../utils/guid';
import studyMetadataManager from '../../utils/studyMetadataManager';
import { measurementApiDefaultConfig } from './../configuration.js';
const configuration = {
...measurementApiDefaultConfig,
...measurementApiDefaultConfig
};
export default class MeasurementApi {
static Instance;
/**
* Set configuration: It should merge default configuration with any new one
*
* @static
* @param {Object} config
* @param {Object} config.server
* @param {string} config.server.type - The server type
* @param {string} config.server.wadoRoot - The server wado URL root
* @param {Array} config.measurementTools
* @param {string} config.measurementTools[].id - The tool group id
* @param {string} config.measurementTools[].name - The tool group name
* @param {Array} config.measurementTools[].childTools - The child tool's configuration
* @param {Object} config.dataExchange
* @param {Function} config.dataExchange.store - Function that store measurement data
* @param {Function} config.dataExchange.retrieve - Function that retrieves measurement data
*
* @memberof MeasurementApi
*/
static setConfiguration(config) {
Object.assign(configuration, config);
}
@ -203,13 +223,14 @@ export default class MeasurementApi {
retrieveMeasurements(patientId, timepointIds) {
const retrievalFn = configuration.dataExchange.retrieve;
const { server } = configuration;
if (typeof retrievalFn !== 'function') {
log.error('Measurement retrieval function has not been configured.');
return;
}
return new Promise((resolve, reject) => {
retrievalFn(patientId, timepointIds).then(measurementData => {
retrievalFn(server).then(measurementData => {
if (measurementData) {
log.info('Measurement data retrieval');
log.info(measurementData);
@ -230,6 +251,10 @@ export default class MeasurementApi {
// Synchronize the new tool data
this.syncMeasurementsAndToolData();
cornerstone.getEnabledElements().forEach(enabledElement => {
cornerstone.updateImage(enabledElement.element);
});
// Let others know that the measurements are updated
this.onMeasurementsUpdated();
}, reject);
@ -237,6 +262,7 @@ export default class MeasurementApi {
}
storeMeasurements(timepointId) {
const { server } = configuration;
const storeFn = configuration.dataExchange.store;
if (typeof storeFn !== 'function') {
log.error('Measurement store function has not been configured.');
@ -278,8 +304,9 @@ export default class MeasurementApi {
};
log.info('Saving Measurements for timepoints:', timepoints);
return storeFn(measurementData, filter).then(() => {
return storeFn(measurementData, filter, server).then(result => {
log.info('Measurement storage completed');
return result;
});
}

44
platform/ui/src/components/measurementTable/MeasurementTable.js
View File

@ -22,8 +22,9 @@ class MeasurementTable extends Component {
onDeleteClick: PropTypes.func,
onEditDescriptionClick: PropTypes.func,
selectedMeasurementNumber: PropTypes.number,
overwallWarnings: PropTypes.object,
t: PropTypes.func,
saveFunction: PropTypes.func,
onSaveComplete: PropTypes.func,
};
static defaultProps = {
@ -38,8 +39,9 @@ class MeasurementTable extends Component {
};
render() {
const hasOverallWarnings =
this.props.overallWarnings.warningList.length > 0;
const { overallWarnings, saveFunction, t } = this.props;
const hasOverallWarnings = overallWarnings.warningList.length > 0;
return (
<div className="measurementTable">
<div className="measurementTableHeader">
@ -55,7 +57,7 @@ class MeasurementTable extends Component {
style={{}}
>
<div className="warningTitle">
{this.props.t('Criteria nonconformities')}
{t('Criteria nonconformities')}
</div>
<div className="warningContent">
{this.getWarningContent()}
@ -75,10 +77,42 @@ class MeasurementTable extends Component {
<ScrollableArea>
<div>{this.getMeasurementsGroups()}</div>
</ScrollableArea>
<div className="measurementTableFooter">
{saveFunction && (
<button onClick={this.saveFunction} className="saveBtn">
<Icon name="save" width="14px" height="14px" />
Save measurements
</button>
)}
</div>
</div>
);
}
saveFunction = async event => {
const { saveFunction, onSaveComplete } = this.props;
if (saveFunction) {
try {
const result = await saveFunction();
if (onSaveComplete) {
onSaveComplete({
title: 'STOW SR',
message: result.message,
type: 'success',
});
}
} catch (error) {
if (onSaveComplete) {
onSaveComplete({
title: 'STOW SR',
message: error.message,
type: 'error',
});
}
}
}
};
getMeasurementsGroups = () => {
return this.props.measurementCollection.map((measureGroup, index) => {
return (
@ -157,7 +191,7 @@ class MeasurementTable extends Component {
};
getWarningContent = () => {
const { warningList = '' } = this.props.overwallWarnings;
const { warningList = '' } = this.props.overallWarnings;
if (Array.isArray(warningList)) {
const listedWarnings = warningList.map((warn, index) => {

145
platform/ui/src/components/measurementTable/MeasurementTable.styl
View File

@ -1,92 +1,117 @@
.measurementTable
background-color: var(--primary-background-color)
height: 100%;
width: 100%;
display: flex;
flex-direction: column;
height: 100%
width: 100%
display: flex
flex-direction: column
.maxMeasurements
border-radius: 3px;
color: var(--primary-background-color);
font-size: 12px;
font-weight: 500;
height: 19px;
line-height: 17px;
margin-top: 22px;
margin-right: 15px;
padding: 2px 6px 0;
text-transform: uppercase;
transition: all 0.3s ease;
background-color: var(--default-color);
border-radius: 3px
color: var(--primary-background-color)
font-size: 12px
font-weight: 500
height: 19px
line-height: 17px
margin-top: 22px
margin-right: 15px
padding: 2px 6px 0
text-transform: uppercase
transition: all 0.3s ease
background-color: var(--default-color)
.measurementTableHeader
padding-left: 45px;
padding-left: 45px
.measurementTableHeaderItem
display: inline-block;
margin-top: 9px;
margin-left: 9px;
padding-left: 9px;
width: 90px;
font-size: 14px;
line-height: 20px;
border-left: 1px solid var(--text-secondary-color);
color: var(--text-primary-color);
display: inline-block
margin-top: 9px
margin-left: 9px
padding-left: 9px
width: 90px
font-size: 14px
line-height: 20px
border-left: 1px solid var(--text-secondary-color)
color: var(--text-primary-color)
.timepointLabel
color: var(--text-secondary-color);
font-size: 12px;
color: var(--text-secondary-color)
font-size: 12px
.warning-status
display: block;
position: absolute;
width: 50px;
height: 40px;
padding-left: 7px;
left: 15px;
top: 7px;
display: block
position: absolute
width: 50px
height: 40px
padding-left: 7px
left: 15px
top: 7px
.warning-border
display: block;
border: 2px solid #e29e4a;
border-radius: 36px;
padding: 6px 7px;
width: 40px;
height: 40px;
display: block
border: 2px solid #e29e4a
border-radius: 36px
padding: 6px 7px
width: 40px
height: 40px
svg
color: #e29e4a;
width: 22px;
height: 20px;
pointer-events: inherit;
color: #e29e4a
width: 22px
height: 20px
pointer-events: inherit
.measurementTableFooter
padding: 10px
color: #fff
text-align: center
z-index: 1
.saveBtn
border: 1px solid var(--ui-border-color-active)
border-radius: 25px
background-color: var(--active-color)
color: var(--ui-gray-dark)
line-height: 25px
padding: 0 20px
outline: none
cursor: pointer
&:hover, &:active
background-color: var(--ui-sky-blue)
svg
margin-right: 4px
position: relative
top: 2px
.tooltip-warning
&.in
opacity 1;
opacity 1
.tooltip-inner
padding: 0
.warningTitle
text-align: left
background-color: var(--ui-gray-darkest);
padding: 7px 15px;
border-top-left-radius: 7px;
border-top-right-radius: 7px;
background-color: var(--ui-gray-darkest)
padding: 7px 15px
border-top-left-radius: 7px
border-top-right-radius: 7px
.warningContent
text-align center
background-color: var(--ui-gray);
border-bottom-left-radius: 7px;
border-bottom-right-radius: 7px;
background-color: var(--ui-gray)
border-bottom-left-radius: 7px
border-bottom-right-radius: 7px
ol
margin-top: auto;
padding-inline-start: 20px;
padding-top: 10px;
padding-bottom: 10px;
padding-left: 25px;
text-align: left;
margin-top: auto
padding-inline-start: 20px
padding-top: 10px
padding-bottom: 10px
padding-left: 25px
text-align: left
li
padding-right: 10px;
padding-right: 10px

2
platform/ui/src/elements/Icon/getIcon.js
View File

@ -62,6 +62,7 @@ import powerOff from './icons/power-off.svg';
import reset from './icons/reset.svg';
import rotate from './icons/rotate.svg';
import rotateRight from './icons/rotate-right.svg';
import saveRegular from './icons/save-regular.svg';
import search from './icons/search.svg';
import searchPlus from './icons/search-plus.svg';
import softTissue from './icons/soft-tissue.svg';
@ -164,6 +165,7 @@ const ICONS = {
'soft-tissue': softTissue,
lung,
liver,
save: saveRegular,
};
/**

11
platform/ui/src/elements/Icon/icons/save-regular.svg Normal file
View File

@ -0,0 +1,11 @@
<svg
aria-hidden="true"
focusable="false"
data-icon="save"
role="img" xmlns="http://www.w3.org/2000/svg"
viewBox="0 0 448 512">
<path
fill="currentColor"
d="M433.941 129.941l-83.882-83.882A48 48 0 0 0 316.118 32H48C21.49 32 0 53.49 0 80v352c0 26.51 21.49 48 48 48h352c26.51 0 48-21.49 48-48V163.882a48 48 0 0 0-14.059-33.941zM272 80v80H144V80h128zm122 352H54a6 6 0 0 1-6-6V86a6 6 0 0 1 6-6h42v104c0 13.255 10.745 24 24 24h176c13.255 0 24-10.745 24-24V83.882l78.243 78.243a6 6 0 0 1 1.757 4.243V426a6 6 0 0 1-6 6zM224 232c-48.523 0-88 39.477-88 88s39.477 88 88 88 88-39.477 88-88-39.477-88-88-88zm0 128c-22.056 0-40-17.944-40-40s17.944-40 40-40 40 17.944 40 40-17.944 40-40 40z">
</path>
</svg>
Side by Side

After

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2
platform/viewer/package.json
View File

@ -60,7 +60,7 @@
"cornerstone-math": "^0.1.8",
"cornerstone-tools": "^4.8.0",
"cornerstone-wado-image-loader": "^3.0.0",
"dcmjs": "^0.6.1",
"dcmjs": "^0.8.2",
"dicom-parser": "^1.8.3",
"dicomweb-client": "^0.4.4",
"hammerjs": "^2.0.8",

115
platform/viewer/src/appExtensions/MeasurementsPanel/ConnectedMeasurementTable.js
View File

@ -3,12 +3,20 @@ import { MeasurementTable } from '@ohif/ui';
import OHIF from '@ohif/core';
import moment from 'moment';
import cornerstone from 'cornerstone-core';
import DICOMSR from './../../lib/DICOMSR';
import jumpToRowItem from './jumpToRowItem.js';
const { setViewportSpecificData } = OHIF.redux.actions;
const { MeasurementApi } = OHIF.measurements;
/**
* Takes a list of objects and a property and return the list grouped by the property
*
* @param {Array} list - The objects to be grouped by
* @param {string} props - The property to group the objects
* @returns {Object}
*/
function groupBy(list, props) {
return list.reduce((a, b) => {
(a[b[props]] = a[b[props]] || []).push(b);
@ -16,16 +24,29 @@ function groupBy(list, props) {
}, {});
}
function getAllTools() {
const config = OHIF.measurements.MeasurementApi.getConfiguration();
/**
* Takes a list of tools grouped and return all tools separately
*
* @param {Array} [toolGroups=[]] - The grouped tools
* @returns {Array} - The list of all tools on all groups
*/
function getAllTools(toolGroups = []) {
let tools = [];
config.measurementTools.forEach(
toolGroups.forEach(
toolGroup => (tools = tools.concat(toolGroup.childTools))
);
return tools;
}
/**
* Takes measurementData and build the measurement text to be used into the table
*
* @param {Object} [measurementData={}]
* @param {string} measurementData.location - The measurement location
* @param {string} measurementData.description - The measurement description
* @returns {string}
*/
function getMeasurementText(measurementData = {}) {
const defaultText = '...';
const { location = '', description = '' } = measurementData;
@ -34,6 +55,14 @@ function getMeasurementText(measurementData = {}) {
return result || defaultText;
}
/**
* Takes a list of measurements grouped by measurement numbers and return each measurement data by available timepoint
*
* @param {Array} measurementNumberList - The list of measurements
* @param {Array} timepoints - The list of available timepoints
* @param {Function} displayFunction - The function that builds the display text by each tool
* @returns
*/
function getDataForEachMeasurementNumber(
measurementNumberList,
timepoints,
@ -56,10 +85,35 @@ function getDataForEachMeasurementNumber(
return data;
}
/**
* Take a measurement toolName and return if any warnings
*
* @param {string} toolName - The tool name
* @returns {string}
*/
function getWarningsForMeasurement(toolName) {
const isToolSupported = DICOMSR.isToolSupported(toolName);
return {
hasWarnings: !isToolSupported,
warningTitle: isToolSupported ? '' : 'Unsupported Tool',
warningList: isToolSupported
? []
: [`${toolName} cannot be persisted at this time`],
};
}
/**
* Take measurements from MeasurementAPI structure and convert into a measurementTable structure
*
* @param {Object} toolCollections - The list of all measurement grouped by groupTool and toolName
* @param {Array} timepoints - The list of available timepoints
* @returns
*/
function convertMeasurementsToTableData(toolCollections, timepoints) {
const config = OHIF.measurements.MeasurementApi.getConfiguration();
const toolGroups = config.measurementTools;
const tools = getAllTools();
const tools = getAllTools(toolGroups);
const tableMeasurements = toolGroups.map(toolGroup => {
return {
@ -88,6 +142,12 @@ function convertMeasurementsToTableData(toolCollections, timepoints) {
} = measurementData;
const measurementId = measurementData._id;
const {
hasWarnings,
warningTitle,
warningList,
} = getWarningsForMeasurement(toolType);
//check if all measurements with same measurementNumber will have same LABEL
const tableMeasurement = {
itemNumber: lesionNamingNumber,
@ -96,10 +156,10 @@ function convertMeasurementsToTableData(toolCollections, timepoints) {
measurementNumber,
lesionNamingNumber,
toolType,
hasWarnings: false, //TODO
warningTitle: '', //TODO
hasWarnings,
warningTitle,
warningList,
isSplitLesion: false, //TODO
warningList: [], //TODO
data: getDataForEachMeasurementNumber(
measurementNumberList,
timepoints,
@ -126,6 +186,13 @@ function convertMeasurementsToTableData(toolCollections, timepoints) {
return tableMeasurements;
}
/**
* Take a list of available timepoints and return a list header information for each timepoint
*
* @param {Array} timepoints - The list of available timepoints
* @param {string} timepoints[].latestDate - The date of the last study taken on the timepoint
* @returns {{label: string, key: string, date: string}[]}
*/
function convertTimepointsToTableData(timepoints) {
if (!timepoints || !timepoints.length) {
return [];
@ -140,8 +207,28 @@ function convertTimepointsToTableData(timepoints) {
];
}
/**
* Takes server type and return a function or undefined
*
* @param {string} serverType - The server type
* @returns {undefined|Function}
*/
function getSaveFunction(serverType) {
if (serverType === 'dicomWeb') {
return () => {
const measurementApi = OHIF.measurements.MeasurementApi.Instance;
const promise = measurementApi.storeMeasurements();
return promise;
};
}
}
const mapStateToProps = state => {
const { timepoints, measurements } = state.timepointManager;
const { timepointManager, servers } = state;
const { timepoints, measurements } = timepointManager;
const activeServer = servers.servers.find(a => a.active === true);
const saveFunction = getSaveFunction(activeServer.type);
return {
timepoints: convertTimepointsToTableData(timepoints),
measurementCollection: convertMeasurementsToTableData(
@ -150,6 +237,7 @@ const mapStateToProps = state => {
),
timepointManager: state.timepointManager,
viewports: state.viewports,
saveFunction,
};
};
@ -265,10 +353,15 @@ const mapDispatchToProps = (dispatch, ownProps) => {
};
const mergeProps = (propsFromState, propsFromDispatch, ownProps) => {
const { timepoints, saveFunction, measurementCollection } = propsFromState;
const { onSaveComplete, selectedMeasurementNumber } = ownProps;
return {
timepoints: propsFromState.timepoints,
measurementCollection: propsFromState.measurementCollection,
selectedMeasurementNumber: ownProps.selectedMeasurementNumber,
timepoints,
saveFunction,
measurementCollection,
onSaveComplete,
selectedMeasurementNumber,
...propsFromDispatch,
onItemClick: (event, measurementData) => {
// TODO: Add timepointId to .data for measurementData?

8
platform/viewer/src/appExtensions/MeasurementsPanel/index.js
View File

@ -11,8 +11,9 @@ export default {
preRegistration({ servicesManager, commandsManager, configuration = {} }) {
init({ servicesManager, commandsManager, configuration });
},
getPanelModule({ servicesManager, commandsManager }) {
const { UILabellingFlowService } = servicesManager.services;
const { UILabellingFlowService, UINotificationService } = servicesManager.services;
const ExtendedConnectedMeasurementTable = () => (
<ConnectedMeasurementTable
onRelabel={tool => {
@ -38,6 +39,11 @@ export default {
});
}
}}
onSaveComplete={message => {
if (UINotificationService) {
UINotificationService.show(message);
}
}}
/>
);
return {

21
platform/viewer/src/connectedComponents/ConnectedViewer.js
View File

@ -1,13 +1,20 @@
import { connect } from "react-redux";
import Viewer from "./Viewer.js";
import OHIF from "@ohif/core";
import { connect } from 'react-redux';
import Viewer from './Viewer.js';
import OHIF from '@ohif/core';
const { setTimepoints, setMeasurements } = OHIF.redux.actions;
const mapStateToProps = (state, ownProps) => {
const getActiveServer = servers => {
const isActive = a => a.active === true;
return servers.servers.find(isActive);
};
const mapStateToProps = state => {
const { viewports, servers } = state;
return {
viewports: state.viewports.viewportSpecificData,
activeViewportIndex: state.viewports.activeViewportIndex
viewports: viewports.viewportSpecificData,
activeViewportIndex: viewports.activeViewportIndex,
activeServer: getActiveServer(servers),
};
};
@ -18,7 +25,7 @@ const mapDispatchToProps = dispatch => {
},
onMeasurementsUpdated: measurements => {
dispatch(setMeasurements(measurements));
}
},
};
};

65
platform/viewer/src/connectedComponents/Viewer.js
View File

@ -11,6 +11,7 @@ import ConnectedStudyBrowser from './ConnectedStudyBrowser.js';
import ConnectedViewerMain from './ConnectedViewerMain.js';
import SidePanel from './../components/SidePanel.js';
import { extensionManager } from './../App.js';
import DICOMSR from '../lib/DICOMSR';
// Contexts
import WhiteLabellingContext from '../context/WhiteLabellingContext.js';
@ -57,21 +58,31 @@ class Viewer extends Component {
static propTypes = {
studies: PropTypes.array,
studyInstanceUids: PropTypes.array,
activeServer: PropTypes.shape({
type: PropTypes.string,
wadoRoot: PropTypes.string,
}),
onTimepointsUpdated: PropTypes.func,
onMeasurementsUpdated: PropTypes.func,
// window.store.getState().viewports.viewportSpecificData
viewports: PropTypes.object.isRequired,
// window.store.getState().viewports.activeViewportIndex
activeViewportIndex: PropTypes.number.isRequired,
isStudyLoaded: PropTypes.bool,
};
constructor(props) {
super(props);
const { activeServer } = this.props;
const server = Object.assign({}, activeServer);
OHIF.measurements.MeasurementApi.setConfiguration({
dataExchange: {
retrieve: this.retrieveMeasurements,
store: this.storeMeasurements,
retrieve: DICOMSR.retrieveMeasurements,
store: DICOMSR.storeMeasurements,
},
server,
});
OHIF.measurements.TimepointApi.setConfiguration({
@ -93,18 +104,6 @@ class Viewer extends Component {
thumbnails: [],
};
retrieveMeasurements = (patientId, timepointIds) => {
OHIF.log.info('retrieveMeasurements');
// TODO: Retrieve the measurements from the latest available SR
return Promise.resolve();
};
storeMeasurements = (measurementData, timepointIds) => {
OHIF.log.info('storeMeasurements');
// TODO: Store the measurements into a new SR sent to the active server
return Promise.resolve();
};
retrieveTimepoints = filter => {
OHIF.log.info('retrieveTimepoints');
@ -171,7 +170,7 @@ class Viewer extends Component {
};
componentDidMount() {
const { studies } = this.props;
const { studies, isStudyLoaded } = this.props;
const { TimepointApi, MeasurementApi } = OHIF.measurements;
const currentTimepointId = 'TimepointId';
@ -191,8 +190,11 @@ class Viewer extends Component {
const patientId = studies[0] && studies[0].patientId;
timepointApi.retrieveTimepoints({ patientId });
measurementApi.retrieveMeasurements(patientId, [currentTimepointId]);
if (isStudyLoaded) {
this.measurementApi.retrieveMeasurements(patientId, [
currentTimepointId,
]);
}
this.setState({
thumbnails: _mapStudiesToThumbnails(studies),
});
@ -200,18 +202,19 @@ class Viewer extends Component {
}
componentDidUpdate(prevProps) {
if (this.props.studies !== prevProps.studies) {
const { studies } = this.props;
const patientId = studies[0] && studies[0].patientId;
const currentTimepointId = this.currentTimepointId;
this.timepointApi.retrieveTimepoints({ patientId });
this.measurementApi.retrieveMeasurements(patientId, [currentTimepointId]);
const { studies, isStudyLoaded } = this.props;
if (studies !== prevProps.studies) {
this.setState({
thumbnails: _mapStudiesToThumbnails(studies),
});
}
if (isStudyLoaded && isStudyLoaded !== prevProps.isStudyLoaded) {
const patientId = studies[0] && studies[0].patientId;
const { currentTimepointId } = this;
this.timepointApi.retrieveTimepoints({ patientId });
this.measurementApi.retrieveMeasurements(patientId, [currentTimepointId]);
}
}
render() {
@ -294,11 +297,11 @@ class Viewer extends Component {
activeIndex={this.props.activeViewportIndex}
/>
) : (
<ConnectedStudyBrowser
studies={this.state.thumbnails}
studyMetadata={this.props.studies}
/>
)}
<ConnectedStudyBrowser
studies={this.state.thumbnails}
studyMetadata={this.props.studies}
/>
)}
</SidePanel>
{/* MAIN */}
@ -334,7 +337,7 @@ export default Viewer;
* @param {Study[]} studies
* @param {DisplaySet[]} studies[].displaySets
*/
const _mapStudiesToThumbnails = function(studies) {
const _mapStudiesToThumbnails = function (studies) {
return studies.map(study => {
const { studyInstanceUid } = study;

8
platform/viewer/src/connectedComponents/ViewerRetrieveStudyData.js
View File

@ -178,6 +178,7 @@ function ViewerRetrieveStudyData({
// hooks
const [error, setError] = useState(false);
const [studies, setStudies] = useState([]);
const [isStudyLoaded, setIsStudyLoaded] = useState(false);
const snackbarContext = useSnackbarContext();
const { appConfig = {} } = useContext(AppContext);
const { filterQueryParam: isFilterStrategy = false } = appConfig;
@ -218,6 +219,7 @@ function ViewerRetrieveStudyData({
);
setStudies([...studies, study]);
setIsStudyLoaded(true);
};
/**
@ -332,7 +334,11 @@ function ViewerRetrieveStudyData({
}
return (
<ConnectedViewer studies={studies} studyInstanceUids={studyInstanceUids} />
<ConnectedViewer
studies={studies}
isStudyLoaded={isStudyLoaded}
studyInstanceUids={studyInstanceUids}
/>
);
}

73
platform/viewer/src/lib/DICOMSR/dataExchange.js Normal file
View File

@ -0,0 +1,73 @@
import { log, studies, utils } from '@ohif/core';
import { retrieveMeasurementFromSR, stowSRFromMeasurements } from './handleStructuredReport';
import findMostRecentStructuredReport from './utils/findMostRecentStructuredReport';
/**
*
* @typedef serverType
* @property {string} type - type of the server
* @property {string} wadoRoot - server wado root url
*
*/
/**
* Function to be registered into MeasurementAPI to retrieve measurements from DICOM Structured Reports
*
* @param {serverType} server
* @returns {Promise} Should resolve with OHIF measurementData object
*/
const retrieveMeasurements = server => {
log.info('[DICOMSR] retrieveMeasurements');
if (!server || server.type !== 'dicomWeb') {
log.error('[DICOMSR] DicomWeb server is required!');
return Promise.reject({});
}
const serverUrl = server.wadoRoot;
const studies = utils.studyMetadataManager.all();
const latestSeries = findMostRecentStructuredReport(studies);
if (!latestSeries) return Promise.resolve({});
return retrieveMeasurementFromSR(latestSeries, studies, serverUrl);
};
/**
* Function to be registered into MeasurementAPI to store measurements into DICOM Structured Reports
*
* @param {Object} measurementData - OHIF measurementData object
* @param {Object} filter
* @param {serverType} server
* @returns {Object} With message to be displayed on success
*/
const storeMeasurements = async (measurementData, filter, server) => {
log.info('[DICOMSR] storeMeasurements');
if (!server || server.type !== 'dicomWeb') {
log.error('[DICOMSR] DicomWeb server is required!');
return Promise.reject({});
}
const serverUrl = server.wadoRoot;
const firstMeasurementKey = Object.keys(measurementData)[0];
const firstMeasurement = measurementData[firstMeasurementKey][0];
const studyInstanceUid =
firstMeasurement && firstMeasurement.studyInstanceUid;
try {
await stowSRFromMeasurements(measurementData, serverUrl);
if (studyInstanceUid) {
studies.deleteStudyMetadataPromise(studyInstanceUid);
}
return {
message: 'Measurements were saved with success',
};
} catch (error) {
log.error(`[DICOMSR] Error while saving the measurements: ${error.message}`);
throw new Error('Error while saving the measurements.');
}
};
export { retrieveMeasurements, storeMeasurements };

84
platform/viewer/src/lib/DICOMSR/handleStructuredReport.js Normal file
View File

@ -0,0 +1,84 @@
import * as dcmjs from 'dcmjs';
import { DICOMWeb } from '@ohif/core';
import parseDicomStructuredReport from './parseDicomStructuredReport';
import parseMeasurementsData from './parseMeasurementsData';
import getAllDisplaySets from './utils/getAllDisplaySets';
import { api } from 'dicomweb-client';
const VERSION_NAME = 'dcmjs-0.0';
const TRANSFER_SYNTAX_UID = '1.2.840.10008.1.2.1';
/**
* Function to retrieve measurements from DICOM Structured Reports coming from determined server
*
* @param {Array} series - List of all series metaData loaded
* @param {Array} studies - List of all studies metaData loaded
* @param {string} serverUrl - Server URL to be used on request
* @returns {Object} MeasurementData
*/
const retrieveMeasurementFromSR = async (series, studies, serverUrl) => {
const config = {
url: serverUrl,
headers: DICOMWeb.getAuthorizationHeader(),
};
const dicomWeb = new api.DICOMwebClient(config);
const instance = series.getFirstInstance();
const options = {
studyInstanceUID: instance.getStudyInstanceUID(),
seriesInstanceUID: instance.getSeriesInstanceUID(),
sopInstanceUID: instance.getSOPInstanceUID(),
};
const part10SRArrayBuffer = await dicomWeb.retrieveInstance(options);
const displaySets = getAllDisplaySets(studies);
const measurementsData = parseDicomStructuredReport(part10SRArrayBuffer, displaySets);
return measurementsData;
};
/**
* Function to store measurements to DICOM Structured Reports in determined server
*
* @param {Object} measurements - OHIF measurementData object
* @param {string} serverUrl - Server URL to be used on request
* @returns {Promise}
*/
const stowSRFromMeasurements = async (measurements, serverUrl) => {
const { dataset } = parseMeasurementsData(
measurements
);
const { DicomMetaDictionary, DicomDict } = dcmjs.data;
const meta = {
FileMetaInformationVersion:
dataset._meta.FileMetaInformationVersion.Value,
MediaStorageSOPClassUID: dataset.SOPClassUID,
MediaStorageSOPInstanceUID: dataset.SOPInstanceUID,
TransferSyntaxUID: TRANSFER_SYNTAX_UID,
ImplementationClassUID: DicomMetaDictionary.uid(),
ImplementationVersionName: VERSION_NAME,
};
const denaturalized = DicomMetaDictionary.denaturalizeDataset(meta);
const dicomDict = new DicomDict(denaturalized);
dicomDict.dict = DicomMetaDictionary.denaturalizeDataset(dataset);
const part10Buffer = dicomDict.write();
const config = {
url: serverUrl,
headers: DICOMWeb.getAuthorizationHeader(),
};
const dicomWeb = new api.DICOMwebClient(config);
const options = {
datasets: [part10Buffer],
};
await dicomWeb.storeInstances(options);
};
export { retrieveMeasurementFromSR, stowSRFromMeasurements };

10
platform/viewer/src/lib/DICOMSR/index.js Normal file
View File

@ -0,0 +1,10 @@
import { retrieveMeasurements, storeMeasurements } from './dataExchange';
import isToolSupported from './utils/isToolSupported';
const DICOMSR = {
retrieveMeasurements,
storeMeasurements,
isToolSupported,
};
export default DICOMSR;

82
platform/viewer/src/lib/DICOMSR/parseDicomStructuredReport.js Normal file
View File

@ -0,0 +1,82 @@
import * as dcmjs from 'dcmjs';
import findInstanceMetadataBySopInstanceUid from './utils/findInstanceMetadataBySopInstanceUid';
/**
* Function to parse the part10 array buffer that comes from a DICOM Structured report into measurementData
* measurementData format is a viewer specific format to be stored into the redux and consumed by other components
* (e.g. measurement table)
*
* @param {ArrayBuffer} part10SRArrayBuffer
* @param {Array} displaySets
* @returns
*/
const parseDicomStructuredReport = (part10SRArrayBuffer, displaySets) => {
// Get the dicom data as an Object
const dicomData = dcmjs.data.DicomMessage.readFile(part10SRArrayBuffer);
const dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(
dicomData.dict
);
const { MeasurementReport } = dcmjs.adapters.Cornerstone;
const storedMeasurementByToolType = MeasurementReport.generateToolState(
dataset
);
const measurementData = {};
let measurementNumber = 0;
Object.keys(storedMeasurementByToolType).forEach(toolName => {
const measurements = storedMeasurementByToolType[toolName];
measurementData[toolName] = [];
measurements.forEach(measurement => {
const instanceMetadata = findInstanceMetadataBySopInstanceUid(
displaySets,
measurement.sopInstanceUid
);
const { _study: study, _series: series } = instanceMetadata;
const { studyInstanceUid, patientId } = study;
const { seriesInstanceUid } = series;
const { sopInstanceUid, frameIndex } = measurement;
const imagePath = getImagePath(studyInstanceUid, seriesInstanceUid, sopInstanceUid, frameIndex);
const imageId = instanceMetadata.getImageId();
if (!imageId) {
return;
}
// TODO: We need the currentTimepointID set into the viewer
const currentTimepointId = 'TimepointId';
const toolData = Object.assign({}, measurement, {
imageId,
imagePath,
seriesInstanceUid,
studyInstanceUid,
patientId,
measurementNumber: ++measurementNumber,
timepointId: currentTimepointId,
toolType: toolName,
_id: imageId + measurementNumber,
});
measurementData[toolName].push(toolData);
});
});
return measurementData;
};
/**
* Function to create imagePath with all imageData related
*
* @param {string} studyInstanceUid
* @param {string} seriesInstanceUid
* @param {string} sopInstanceUid
* @param {string} frameIndex
* @returns
*/
const getImagePath = (studyInstanceUid, seriesInstanceUid, sopInstanceUid, frameIndex) => {
return [studyInstanceUid, seriesInstanceUid, sopInstanceUid, frameIndex].join('_');
}
export default parseDicomStructuredReport;

55
platform/viewer/src/lib/DICOMSR/parseMeasurementsData.js Normal file
View File

@ -0,0 +1,55 @@
import * as dcmjs from 'dcmjs';
import { log, measurements } from '@ohif/core';
import cornerstone from 'cornerstone-core';
import isToolSupported from './utils/isToolSupported';
/**
* Function to parse OHIF viewer measurementData into a dcmjs MeasurementReport
*
* @param {Object} measurementsData - OHIF measurementData object
* @returns {Object} Dataset: measurement report from dcmjs
*/
const parseMeasurementsData = measurementsData => {
const { MeasurementReport } = dcmjs.adapters.Cornerstone;
const { getImageIdForImagePath } = measurements;
const toolState = {};
const unsupportedTools = [];
Object.keys(measurementsData).forEach(measurementType => {
const annotations = measurementsData[measurementType];
annotations.forEach(annotation => {
const { toolType, imagePath } = annotation;
if (isToolSupported(toolType)) {
const imageId = getImageIdForImagePath(imagePath);
toolState[imageId] = toolState[imageId] || {};
toolState[imageId][toolType] = toolState[imageId][toolType] || {
data: [],
};
toolState[imageId][toolType].data.push(annotation);
} else {
unsupportedTools.push(toolType);
}
});
});
if (unsupportedTools.length > 0) {
log.warn(
`[DICOMSR] Tooltypes not supported: ${unsupportedTools.join(', ')}`
);
}
const report = MeasurementReport.generateReport(
toolState,
cornerstone.metaData
);
return {
dataset: report.dataset,
};
};
export default parseMeasurementsData;

22
platform/viewer/src/lib/DICOMSR/utils/findInstanceMetadataBySopInstanceUid.js Normal file
View File

@ -0,0 +1,22 @@
/**
* Should Find the requested instance metadata into the displaySets and return
*
* @param {Array} displaySets - List of displaySets
* @param {string} sopInstanceUid - sopInstanceUID to look for
* @returns {Object} - instance metadata found
*/
const findInstanceMetadataBySopInstanceUid = (displaySets, sopInstanceUid) => {
let instanceFound;
displaySets.find(displaySet => {
if (!displaySet.images) return false;
instanceFound = displaySet.images.find(instanceMetadata => instanceMetadata._sopInstanceUID === sopInstanceUid);
return !!instanceFound;
});
return instanceFound;
};
export default findInstanceMetadataBySopInstanceUid;

57
platform/viewer/src/lib/DICOMSR/utils/findMostRecentStructuredReport.js Normal file
View File

@ -0,0 +1,57 @@
/**
* Should find the most recent Structured Report metadata
*
* @param {Array} studies
* @returns {Object} Series
*/
const findMostRecentStructuredReport = (studies) => {
let mostRecentStructuredReport;
studies.forEach(study => {
const allSeries = study.getSeries ? study.getSeries() : [];
allSeries.forEach(series => {
if (isStructuredReportSeries(series)) {
if (!mostRecentStructuredReport || compareSeriesDate(series, mostRecentStructuredReport)) {
mostRecentStructuredReport = series;
}
}
});
});
return mostRecentStructuredReport;
};
/**
* Checks if series sopClassUID matches with the supported Structured Reports sopClassUID
*
* @param {Object} series - Series metadata
* @returns {boolean}
*/
const isStructuredReportSeries = (series) => {
const supportedSopClassUIDs = [
'1.2.840.10008.5.1.4.1.1.88.22',
'1.2.840.10008.5.1.4.1.1.11.1',
];
const firstInstance = series.getFirstInstance();
const sopClassUid = firstInstance._instance.sopClassUid;
return supportedSopClassUIDs.includes(sopClassUid);
}
/**
* Checkes if series1 is newer than series2
*
* @param {Object} series1 - Series Metadata 1
* @param {Object} series2 - Series Metadata 2
* @returns {boolean} true/false if series1 is newer than series2
*/
const compareSeriesDate = (series1, series2) => {
return series1._data.seriesDate > series2._data.seriesDate ||
(series1._data.seriesDate === series2._data.seriesDate &&
series1._data.seriesTime > series2._data.seriesTime);
}
export default findMostRecentStructuredReport;

19
platform/viewer/src/lib/DICOMSR/utils/getAllDisplaySets.js Normal file
View File

@ -0,0 +1,19 @@
/**
* Retrieve a list of all displaySets of all studies
*
* @param {Object} studies - List of studies loaded into the viewer
* @returns {Object} List of DisplaySets
*/
const getAllDisplaySets = (studies) => {
let allDisplaySets = [];
studies.forEach(study => {
if (study.getDisplaySets) {
allDisplaySets = allDisplaySets.concat(study.getDisplaySets());
}
});
return allDisplaySets;
};
export default getAllDisplaySets;

14
platform/viewer/src/lib/DICOMSR/utils/isToolSupported.js Normal file
View File

@ -0,0 +1,14 @@
import * as dcmjs from 'dcmjs';
/**
* Checks if dcmjs has support to determined tool
*
* @param {string} toolName
* @returns {boolean}
*/
const isToolSupported = toolName => {
const adapter = dcmjs.adapters.Cornerstone;
return !!adapter[toolName];
};
export default isToolSupported;

18
yarn.lock
View File

@ -876,7 +876,7 @@
core-js "^2.6.5"
regenerator-runtime "^0.13.2"
"@babel/polyfill@^7.0.0", "@babel/polyfill@^7.2.5":
"@babel/polyfill@^7.0.0", "@babel/polyfill@^7.6.0":
version "7.6.0"
resolved "https://registry.yarnpkg.com/@babel/polyfill/-/polyfill-7.6.0.tgz#6d89203f8b6cd323e8d946e47774ea35dc0619cc"
integrity sha512-q5BZJI0n/B10VaQQvln1IlDK3BTBJFbADx7tv+oXDPIDZuTo37H5Adb9jhlXm/fEN4Y7/64qD9mnrJJG7rmaTw==
@ -6535,14 +6535,14 @@ dateformat@^3.0.0:
resolved "https://registry.yarnpkg.com/dateformat/-/dateformat-3.0.3.tgz#a6e37499a4d9a9cf85ef5872044d62901c9889ae"
integrity sha512-jyCETtSl3VMZMWeRo7iY1FL19ges1t55hMo5yaam4Jrsm5EPL89UQkoQRyiI+Yf4k8r2ZpdngkV8hr1lIdjb3Q==
dcmjs@^0.6.1:
version "0.6.1"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.6.1.tgz#453f764bca2cd8e3430126ba8385ef4c77071bcd"
integrity sha512-sJ0cRVZY02GSaAW5S9JPcv8+7iDtgrM0L/niYWAvu2piSa4bFSXwKi+t4XevAfkm+mF0sXZtaD15bw+/oiCYkw==
dcmjs@^0.8.2:
version "0.8.2"
resolved "https://registry.yarnpkg.com/dcmjs/-/dcmjs-0.8.2.tgz#e1107273764de0a3052244b79d999fd870e58650"
integrity sha512-HEd1Rq12qxZXVXr5B4xgl/foCWaXxioO5v42FLgiUjKrbQR6iKIVcZsmE+3/AvAurcHiQFfW5vk5K4AY7eAp5A==
dependencies:
"@babel/polyfill" "^7.2.5"
"@babel/runtime" "^7.3.1"
loglevelnext "^3.0.0"
"@babel/polyfill" "^7.6.0"
"@babel/runtime" "^7.6.3"
loglevelnext "^3.0.1"
ndarray "^1.0.18"
debug@2.6.9, debug@^2.2.0, debug@^2.3.3, debug@^2.6.0, debug@^2.6.1, debug@^2.6.3, debug@^2.6.6, debug@^2.6.8, debug@^2.6.9:
@ -12373,7 +12373,7 @@ loglevelnext@^1.0.1, loglevelnext@^1.0.2:
es6-symbol "^3.1.1"
object.assign "^4.1.0"
loglevelnext@^3.0.0:
loglevelnext@^3.0.1:
version "3.0.1"
resolved "https://registry.yarnpkg.com/loglevelnext/-/loglevelnext-3.0.1.tgz#e3e4659c4061c09264f6812c33586dc55a009a04"
integrity sha512-JpjaJhIN1reaSb26SIxDGtE0uc67gPl19OMVHrr+Ggt6b/Vy60jmCtKgQBrygAH0bhRA2nkxgDvM+8QvR8r0YA==