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feat(STOW-RS) Save DICOM Structured Reports from Measurement Table back to archive (#236)

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* Small refactor into Table Class setting events as static object into class

* feature(STOW-SR) : Initial changes to stow when we have Server.

* Improvements into requests and small fix into style

* Small fix for jumpToRow without refheshing page

* Handling STOW-SR once we don't have server

* feature(STOW-SR) Refactor

* Merge request with makeRequest and delete old file

* Expose wadoproxy to client and update measurement-table to start using wadoproxy.getServerUrl

* Move WADOProxy.getServerUrl to Measurement-table package. Fix querystring issue.

* Remove proxy:enabled in favour of requestOptions.requestFromBrowser

* Bcrypt 2.0.0 to fix Travis
This commit is contained in:
Gustavo André Lelis 2018-07-31 10:01:26 -03:00 committed by Erik Ziegler
parent 13e4dc25e1
commit 26b14f1dab
26 changed files with 1079 additions and 179 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
OHIFViewer/client/components/viewer/viewer.js
View File

@ -4,7 +4,7 @@ import { Template } from 'meteor/templating';
import { ReactiveDict } from 'meteor/reactive-dict';
import { Tracker } from 'meteor/tracker';
import { OHIF } from 'meteor/ohif:core';
import { MeasurementTable, measurementEvents } from 'meteor/ohif:measurement-table';
import { MeasurementTable } from 'meteor/ohif:measurement-table';
import 'meteor/ohif:cornerstone';
import 'meteor/ohif:viewerbase';
@ -168,7 +168,7 @@ Template.viewer.onRendered(function() {
Template.viewer.events( Object.assign({
// Viewer Events
},
measurementEvents
MeasurementTable.measurementEvents
));
Template.viewer.onDestroyed(function() {

440
OHIFViewer/package-lock.json generated
View File

@ -34,6 +34,436 @@
"integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=",
"dev": true
},
"bcrypt": {
"version": "3.0.0",
"resolved": "https://registry.npmjs.org/bcrypt/-/bcrypt-3.0.0.tgz",
"integrity": "sha512-gjicxsD4e5U3nH0EqiEb5y+fKpsZ7F52wcnmNfu45nxnolWVAYh7NgbdfilY+5x1v6cLspxmzz4hf+ju2pFxhA==",
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}
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"process-nextick-args": "~2.0.0",
"safe-buffer": "~5.1.1",
"string_decoder": "~1.0.3",
"util-deprecate": "~1.0.1"
}
},
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"version": "2.6.2",
"bundled": true,
"requires": {
"glob": "^7.0.5"
}
},
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"version": "5.1.1",
"bundled": true
},
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"version": "2.1.2",
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},
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"version": "1.2.4",
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},
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},
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},
"signal-exit": {
"version": "3.0.2",
"bundled": true
},
"string-width": {
"version": "1.0.2",
"bundled": true,
"requires": {
"code-point-at": "^1.0.0",
"is-fullwidth-code-point": "^1.0.0",
"strip-ansi": "^3.0.0"
}
},
"string_decoder": {
"version": "1.0.3",
"bundled": true,
"requires": {
"safe-buffer": "~5.1.0"
}
},
"strip-ansi": {
"version": "3.0.1",
"bundled": true,
"requires": {
"ansi-regex": "^2.0.0"
}
},
"strip-json-comments": {
"version": "2.0.1",
"bundled": true
},
"tar": {
"version": "4.4.4",
"bundled": true,
"requires": {
"chownr": "^1.0.1",
"fs-minipass": "^1.2.5",
"minipass": "^2.3.3",
"minizlib": "^1.1.0",
"mkdirp": "^0.5.0",
"safe-buffer": "^5.1.2",
"yallist": "^3.0.2"
},
"dependencies": {
"safe-buffer": {
"version": "5.1.2",
"bundled": true
},
"yallist": {
"version": "3.0.2",
"bundled": true
}
}
},
"util-deprecate": {
"version": "1.0.2",
"bundled": true
},
"wide-align": {
"version": "1.1.3",
"bundled": true,
"requires": {
"string-width": "^1.0.2 || 2"
}
},
"wrappy": {
"version": "1.0.2",
"bundled": true
}
}
},
"brace-expansion": {
"version": "1.1.11",
"resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz",
@ -228,6 +658,11 @@
"integrity": "sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=",
"dev": true
},
"nan": {
"version": "2.10.0",
"resolved": "https://registry.npmjs.org/nan/-/nan-2.10.0.tgz",
"integrity": "sha512-bAdJv7fBLhWC+/Bls0Oza+mvTaNQtP+1RyhhhvD95pgUJz6XM5IzgmxOkItJ9tkoCiplvAnXI1tNmmUD/eScyA=="
},
"once": {
"version": "1.4.0",
"resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz",
@ -298,6 +733,11 @@
"util-deprecate": "~1.0.1"
}
},
"regenerator-runtime": {
"version": "0.11.1",
"resolved": "https://registry.npmjs.org/regenerator-runtime/-/regenerator-runtime-0.11.1.tgz",
"integrity": "sha512-MguG95oij0fC3QV3URf4V2SDYGJhJnJGqvIIgdECeODCT98wSWDAJ94SSuVpYQUoTcGUIL6L4yNB7j1DFFHSBg=="
},
"rimraf": {
"version": "2.6.2",
"resolved": "https://registry.npmjs.org/rimraf/-/rimraf-2.6.2.tgz",

1
OHIFViewer/package.json
View File

@ -5,6 +5,7 @@
"main": "index.js",
"dependencies": {
"@babel/runtime": "7.0.0-beta.51",
"bcrypt": "^2.0.0",
"loglevel": "^1.6.1"
},
"devDependencies": {

8
Packages/ohif-dicomweb-client/src/makeRequest.js
View File

@ -29,6 +29,14 @@ async function makeRequest(url, options) {
});
}
if(options.method) {
requestOpt.method = options.method;
}
if (options.method === 'POST' && options.body) {
requestOpt.body = options.body;
}
return new Promise((resolve, reject) => {
// TODO: Kept getting weird build errors from RegExp
const isAbsolute = parsed.href.indexOf('http://') === 0 || parsed.href.indexOf('https://') === 0;

17
Packages/ohif-measurement-table/client/configuration/dataExchange.js
View File

@ -1,5 +1,6 @@
import { OHIF } from 'meteor/ohif:core';
import { handleSR, getLatestSRSeries } from "../utils/handleSR";
import { retrieveMeasurementFromSR, stowSRFromMeasurements } from '../utils/handleSR';
import { getLatestSRSeries } from '../utils/srUtils';
export const retrieveMeasurements = (patientId, timepointIds) => {
OHIF.log.info('retrieveMeasurements');
@ -8,7 +9,7 @@ export const retrieveMeasurements = (patientId, timepointIds) => {
if(!latestSeries) return Promise.resolve({});
return handleSR(latestSeries).then((value) => {
return retrieveMeasurementFromSR(latestSeries).then((value) => {
return {
length: value
}
@ -17,11 +18,17 @@ export const retrieveMeasurements = (patientId, timepointIds) => {
export const storeMeasurements = (measurementData, timepointIds) => {
OHIF.log.info('storeMeasurements');
const server = OHIF.servers.getCurrentServer();
if (!server || server.type !== 'dicomWeb') {
return Promise.resolve({});
}
// Here is where we should do any required data transformation and API calls
const studyInstanceUid = measurementData[Object.keys(measurementData)[0]][0].studyInstanceUid
// TODO: Write SR, STOW back to PACS
return Promise.resolve();
return stowSRFromMeasurements(measurementData).then( () => {
OHIF.studies.deleteStudyMetadataPromise(studyInstanceUid);
});
};
export const retrieveTimepoints = filter => {

42
Packages/ohif-measurement-table/client/index.js
View File

@ -1,7 +1,6 @@
import { OHIF } from 'meteor/ohif:core';
import { Session } from 'meteor/session';
import { configureApis } from './configuration/configuration'
import { $ } from 'meteor/jquery';
class MeasurementTable {
constructor() {
@ -9,8 +8,6 @@ class MeasurementTable {
Session.set('TimepointsReady', false);
Session.set('MeasurementsReady', false);
this.firstMeasurementActivated = false;
}
async onCreated(instance) {
@ -38,6 +35,8 @@ class MeasurementTable {
measurementApi.syncMeasurementsAndToolData();
this.firstMeasurementActivated = false;
instance.autorun(() => {
if (!Session.get('TimepointsReady') ||
!Session.get('MeasurementsReady') ||
@ -100,26 +99,25 @@ class MeasurementTable {
this.firstMeasurementActivated = true;
}
};
const measurementEvents = {
'cornerstonetoolsmeasurementadded .imageViewerViewport'(event, instance) {
const originalEvent = event.originalEvent;
OHIF.measurements.MeasurementHandlers.onAdded(originalEvent, instance);
},
'cornerstonetoolsmeasurementmodified .imageViewerViewport'(event, instance) {
const originalEvent = event.originalEvent;
instance.measurementModifiedHandler(originalEvent, instance);
},
'cornerstonemeasurementremoved .imageViewerViewport'(event, instance) {
const originalEvent = event.originalEvent;
OHIF.measurements.MeasurementHandlers.onRemoved(originalEvent, instance);
}
static measurementEvents = {
'cornerstonetoolsmeasurementadded .imageViewerViewport'(event, instance) {
const originalEvent = event.originalEvent;
OHIF.measurements.MeasurementHandlers.onAdded(originalEvent, instance);
},
'cornerstonetoolsmeasurementmodified .imageViewerViewport'(event, instance) {
const originalEvent = event.originalEvent;
instance.measurementModifiedHandler(originalEvent, instance);
},
'cornerstonemeasurementremoved .imageViewerViewport'(event, instance) {
const originalEvent = event.originalEvent;
OHIF.measurements.MeasurementHandlers.onRemoved(originalEvent, instance);
}
};
};
export {
MeasurementTable,
measurementEvents
MeasurementTable
}

22
Packages/ohif-measurement-table/client/utils/getLengthMeasurementData.js
View File

@ -1,26 +1,8 @@
import { OHIF } from 'meteor/ohif:core';
import { cornerstone } from 'meteor/ohif:cornerstone';
import { getInstanceMetadata } from './srUtils';
function getInstanceMetadata (displaySets, sopInstanceUid) {
let instance;
// Use Array.some so that this loop stops when the internal loop
// has found the correct instance
displaySets.some(displaySet => {
// Search the display set to find the instance metadata for
return displaySet.images.find(instanceMetadata => {
if (instanceMetadata._sopInstanceUID === sopInstanceUid) {
instance = instanceMetadata;
return true;
}
});
});
return instance;
};
export default function getLengthMeasurementData(lengthMeasurementContent, displaySets) {
export default getLengthMeasurementData = (lengthMeasurementContent, displaySets) => {
let lengthStates = [];
lengthMeasurementContent.forEach(groupItemContent => {

79
Packages/ohif-measurement-table/client/utils/getLengthMeasurementGroupContentItem.js Normal file
View File

@ -0,0 +1,79 @@
export default measurementGroupContentItem = (measurement, sopClassUid) => {
const {
handles,
length,
frameIndex,
sopInstanceUid
} = measurement;
const measurementContentItem = [
{
RelationshipType: 'HAS OBS CONTEXT',
ValueType: 'TEXT',
ConceptNameCodeSequence: {
CodeValue: '112039',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Tracking Identifier',
},
TextValue: 'web annotation',
},
{
RelationshipType: 'HAS OBS CONTEXT',
ValueType: 'UIDREF',
ConceptNameCodeSequence: {
CodeValue: '112040',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Tracking Unique Identifier',
},
UID: dcmjs.data.DicomMetaDictionary.uid(),
},
{
RelationshipType: 'CONTAINS',
ValueType: 'CODE',
ConceptNameCodeSequence: {
CodeValue: '121071',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Finding',
},
ConceptCodeSequence: {
CodeValue: 'SAMPLEFINDING',
CodingSchemeDesignator: '99dcmjs',
CodeMeaning: 'Sample Finding',
},
},
{
RelationshipType: 'CONTAINS',
ValueType: 'NUM',
ConceptNameCodeSequence: {
CodeValue: 'G-D7FE',
CodingSchemeDesignator: 'SRT',
CodeMeaning: 'Length',
},
MeasuredValueSequence: {
MeasurementUnitsCodeSequence: {
CodeValue: 'mm',
CodingSchemeDesignator: 'UCUM',
CodingSchemeVersion: '1.4',
CodeMeaning: 'millimeter',
},
NumericValue: length,
},
ContentSequence: {
RelationshipType: 'INFERRED FROM',
ValueType: 'SCOORD',
GraphicType: 'POLYLINE',
GraphicData: [ handles.start.x, handles.start.y, handles.end.x, handles.end.y ],
ContentSequence: {
RelationshipType: 'SELECTED FROM',
ValueType: 'IMAGE',
ReferencedSOPSequence: {
ReferencedSOPClassUID: sopClassUid,
ReferencedSOPInstanceUID: sopInstanceUid,
ReferencedFrameNumber: frameIndex,
}
},
},
},
];
return measurementContentItem;
};

153
Packages/ohif-measurement-table/client/utils/handleSR.js
View File

@ -1,100 +1,63 @@
import { OHIF } from 'meteor/ohif:core';
import { dcmjs } from 'meteor/ohif:cornerstone';
import getLengthMeasurementData from './getLengthMeasurementData';
import retrieveDataFromSR from './retrieveDataFromSR';
import retrieveDataFromMeasurements from './retrieveDataFromMeasurements';
import {
multipartEncode
} from './srUtils';
const supportedSopClassUIDs = ['1.2.840.10008.5.1.4.1.1.88.22'];
const toArray = function(x) {
return (x.constructor.name === "Array" ? x : [x]);
};
const codeMeaningEquals = (codeMeaningName) => {
return (contentItem) => {
return contentItem.ConceptNameCodeSequence.CodeMeaning === codeMeaningName;
};
};
const imagingMeasurementsToMeasurementData = (dataset, displaySets) => {
// Identify the Imaging Measurements
const imagingMeasurementContent = toArray(dataset.ContentSequence).find(codeMeaningEquals("Imaging Measurements"));
// Retrieve the Measurements themselves
const measurementGroupContent = toArray(imagingMeasurementContent.ContentSequence).find(codeMeaningEquals("Measurement Group"));
// For now, bail out if the dataset is not a TID1500 SR with length measurements
// TODO: generalize to the various kinds of report
// TODO: generalize to the kinds of measurements the Viewer supports
if (dataset.ContentTemplateSequence.TemplateIdentifier !== "1500") {
OHIF.log.warn("This package can currently only interpret DICOM SR TID 1500");
return {};
}
// Filter to find Length measurements in the Structured Report
const lengthMeasurementContent = toArray(measurementGroupContent.ContentSequence).filter(codeMeaningEquals("Length"));
// Retrieve Length Measurement Data
return getLengthMeasurementData(lengthMeasurementContent, displaySets);
};
const retrieveDataFromSR = (Part10SRArrayBuffer) => {
const allStudies = OHIF.viewer.Studies.all();
let allDisplaySets = [];
allStudies.forEach(study => {
allDisplaySets = allDisplaySets.concat(study.displaySets);
});
// get the dicom data as an Object
let dicomData = dcmjs.data.DicomMessage.readFile(Part10SRArrayBuffer);
let dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(dicomData.dict);
// Convert the SR into the kind of object the Measurements package is expecting
return imagingMeasurementsToMeasurementData(dataset, allDisplaySets);
};
export const getLatestSRSeries = () => {
const allStudies = OHIF.viewer.StudyMetadataList.all();
let latestSeries;
allStudies.forEach(study => {
study.getSeries().forEach(series => {
const firstInstance = series.getFirstInstance();
const sopClassUid = firstInstance._instance.sopClassUid;
if (supportedSopClassUIDs.includes(sopClassUid)) {
if(!latestSeries) {
latestSeries = series;
} else if (series._data.seriesDate > latestSeries._data.seriesDate ||
(series._data.seriesDate === latestSeries._data.seriesDate && series._data.seriesTime > latestSeries._data.seriesTime)) {
latestSeries = series;
}
}
});
});
return latestSeries;
};
export const handleSR = (series) => {
const retrieveMeasurementFromSR = async (series) => {
const instance = series.getFirstInstance();
const options = {
method: 'GET',
responseType: 'arraybuffer',
};
const url = instance.getDataProperty('wadouri');
return new Promise((resolve, reject) => {
const request = new XMLHttpRequest();
request.responseType = 'arraybuffer';
request.open('GET', instance.getDataProperty('wadouri'));
request.onload = function (progressEvent) {
const data = retrieveDataFromSR(progressEvent.currentTarget.response);
resolve(data);
};
request.onerror = function(error) {
reject(error);
};
request.send();
});
try {
const result = await DICOMWeb.makeRequest(url, options);
const data = await result.arrayBuffer();
const measurementData = retrieveDataFromSR(data);
return Promise.resolve(measurementData);
} catch(error) {
return Promise.reject(error);
}
};
/**
* Retrieve the DICOMWeb STOW-RS URL for the current server.
*
* See ftp://medical.nema.org/medical/dicom/current/output/html/part18.html#sect_6.6.1.1
*
* @return {string|null} The URL, rerouted to the proxy if the WADOProxy is enabled.
*/
function getStowRsUrl() {
const server = OHIF.servers.getCurrentServer();
const url = `${server.wadoRoot}/studies`;
return WADOProxy.convertURL(url, server);
}
const stowSRFromMeasurements = async (measurements) => {
const serverUrl = getStowRsUrl();
const reportDataset = retrieveDataFromMeasurements(measurements);
const boundary = dcmjs.data.DicomMetaDictionary.uid();
const options = {
method: 'POST',
body: multipartEncode(reportDataset, boundary),
headers: {
'Content-Type': `multipart/related; type=application/dicom; boundary=${boundary}`
}
};
try {
await DICOMWeb.makeRequest(serverUrl, options);
return Promise.resolve();
} catch(error) {
return Promise.reject(error);
}
};
export {
retrieveMeasurementFromSR,
stowSRFromMeasurements
}

199
Packages/ohif-measurement-table/client/utils/retrieveDataFromMeasurements.js Normal file
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@ -0,0 +1,199 @@
import { dcmjs } from 'meteor/ohif:cornerstone';
import { getInstanceMetadata, getAllDisplaySets } from './srUtils';
import getLengthMeasurementGroupContentItem from './getLengthMeasurementGroupContentItem';
export default retrieveDataFromMeasurements = (measurements) => {
const { studyInstanceUid, seriesInstanceUid, sopInstanceUid } = measurements.allTools[0];
const displaySets = getAllDisplaySets();
const instanceMetadata = getInstanceMetadata(displaySets, sopInstanceUid);
const sopClassUid = instanceMetadata._data.sopClassUid;
// TODO: figure out what is needed to make a dcmjs dataset from
// information available in the viewer. Apparently the raw dicom is not available
// directly.
const derivationSourceDataset = {
StudyInstanceUID: studyInstanceUid,
SeriesInstanceUID: seriesInstanceUid,
SOPInstanceUID: sopInstanceUid,
SOPClassUID: sopClassUid
};
report = new dcmjs.derivations.StructuredReport([derivationSourceDataset]);
dataset = report.dataset;
// TODO: what is the correct metaheader
// http://dicom.nema.org/medical/Dicom/current/output/chtml/part10/chapter_7.html
// TODO: move meta creation to dcmjs
const fileMetaInformationVersionArray = new Uint16Array(1);
fileMetaInformationVersionArray[0] = 1;
dataset._meta = {
FileMetaInformationVersion: fileMetaInformationVersionArray.buffer,
MediaStorageSOPClassUID: dataset.SOPClassUID,
MediaStorageSOPInstanceUID: dataset.SOPInstanceUID,
TransferSyntaxUID: "1.2.840.10008.1.2.1", // Explicit little endian (always for dcmjs?)
ImplementationClassUID: dcmjs.data.DicomMetaDictionary.uid(), // TODO: could be git hash or other valid id
ImplementationVersionName: "OHIFViewer"
};
// TODO: factor out a lot of this back into dcmjs for use in both
// the example and in the Viewer
const measurementGroupContentSequence = [];
for (measurement of measurements.allTools) {
if (measurement.toolType === 'length') {
measurementGroupContentSequence.push.apply(measurementGroupContentSequence, getLengthMeasurementGroupContentItem(measurement, sopClassUid));
}
}
// TODO: make a TID1550 derivation as an SR subclass
dataset = Object.assign(dataset, {
ConceptNameCodeSequence: {
CodeValue: '126000',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Imaging Measurement Report'
},
ContinuityOfContent: 'SEPARATE',
PerformedProcedureCodeSequence: [],
CompletionFlag: 'COMPLETE',
VerificationFlag: 'UNVERIFIED',
ReferencedPerformedProcedureStepSequence: [],
InstanceNumber: 1,
CurrentRequestedProcedureEvidenceSequence: {
StudyInstanceUID: dataset.StudyInstanceUID,
ReferencedSeriesSequence: {
SeriesInstanceUID: dataset.SeriesInstanceUID,
ReferencedSOPSequence: {
ReferencedSOPClassUID: derivationSourceDataset.SOPClassUID,
ReferencedSOPInstanceUID: derivationSourceDataset.SOPInstanceUID
},
},
},
CodingSchemeIdentificationSequence: {
CodingSchemeDesignator: "99dcmjs",
CodingSchemeName: "Codes used for dcmjs",
CodingSchemeVersion: "0",
CodingSchemeResponsibleOrganization: "https://github.com/pieper/dcmjs"
},
ContentTemplateSequence: {
MappingResource: 'DCMR',
TemplateIdentifier: '1500'
},
ContentSequence: [
{
RelationshipType: 'HAS CONCEPT MOD',
ValueType: 'CODE',
ConceptNameCodeSequence: {
CodeValue: '121049',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Language of Content Item and Descendants',
},
ConceptCodeSequence: {
CodeValue: 'eng',
CodingSchemeDesignator: 'RFC3066',
CodeMeaning: 'English',
},
ContentSequence: {
RelationshipType: 'HAS CONCEPT MOD',
ValueType: 'CODE',
ConceptNameCodeSequence: {
CodeValue: '121046',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Country of Language',
},
ConceptCodeSequence: {
CodeValue: 'US',
CodingSchemeDesignator: 'ISO3166_1',
CodeMeaning: 'United States',
}
}
},
{
RelationshipType: 'HAS OBS CONTEXT',
ValueType: 'PNAME',
ConceptNameCodeSequence: {
CodeValue: '121008',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Person Observer Name',
},
PersonName: 'user^web' // TODO: these can be options argument for constructor
},
{
RelationshipType: 'HAS OBS CONTEXT',
ValueType: 'TEXT',
ConceptNameCodeSequence: {
CodeValue: 'RP-100006',
CodingSchemeDesignator: '99dcmjs',
CodeMeaning: "Person Observer's Login Name"
},
TextValue: 'user'
},
{
RelationshipType: 'HAS CONCEPT MOD',
ValueType: 'CODE',
ConceptNameCodeSequence: {
CodeValue: '121058',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Procedure reported'
},
ConceptCodeSequence: {
CodeValue: '1',
CodingSchemeDesignator: '99dcmjs',
CodeMeaning: 'Unknown procedure'
},
},
{
RelationshipType: 'CONTAINS',
ValueType: 'CONTAINER',
ConceptNameCodeSequence: {
CodeValue: '111028',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Image Library',
},
ContinuityOfContent: 'SEPARATE',
ContentSequence: {
RelationshipType: 'CONTAINS',
ValueType: 'CONTAINER',
ConceptNameCodeSequence: {
CodeValue: '126200',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Image Library Group',
},
ContinuityOfContent: 'SEPARATE',
ContentSequence: {
RelationshipType: 'CONTAINS',
ValueType: 'IMAGE',
ReferencedSOPSequence: {
// TODO: this should refer to the UIDs extracted from the toolState / instance info
ReferencedSOPClassUID: dataset.SOPClassUID,
ReferencedSOPInstanceUID: dataset.SOPInstanceUID,
},
},
},
},
{
RelationshipType: 'CONTAINS',
ValueType: 'CONTAINER',
ConceptNameCodeSequence: {
CodeValue: '126010',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Imaging Measurements', // TODO: would be nice to abstract the code sequences (in a dictionary? a service?)
},
ContinuityOfContent: 'SEPARATE',
ContentSequence: {
RelationshipType: 'CONTAINS',
ValueType: 'CONTAINER',
ConceptNameCodeSequence: {
CodeValue: '125007',
CodingSchemeDesignator: 'DCM',
CodeMeaning: 'Measurement Group',
},
ContinuityOfContent: 'SEPARATE',
ContentSequence: measurementGroupContentSequence,
},
},
]
});
return dataset;
}

37
Packages/ohif-measurement-table/client/utils/retrieveDataFromSR.js Normal file
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@ -0,0 +1,37 @@
import { dcmjs } from 'meteor/ohif:cornerstone';
import getLengthMeasurementData from './getLengthMeasurementData';
import { toArray, codeMeaningEquals, getAllDisplaySets } from './srUtils'
const imagingMeasurementsToMeasurementData = (dataset, displaySets) => {
// Identify the Imaging Measurements
const imagingMeasurementContent = toArray(dataset.ContentSequence).find(codeMeaningEquals("Imaging Measurements"));
// Retrieve the Measurements themselves
const measurementGroupContent = toArray(imagingMeasurementContent.ContentSequence).find(codeMeaningEquals("Measurement Group"));
// For now, bail out if the dataset is not a TID1500 SR with length measurements
// TODO: generalize to the various kinds of report
// TODO: generalize to the kinds of measurements the Viewer supports
if (dataset.ContentTemplateSequence.TemplateIdentifier !== "1500") {
OHIF.log.warn("This package can currently only interpret DICOM SR TID 1500");
return {};
}
// Filter to find Length measurements in the Structured Report
const lengthMeasurementContent = toArray(measurementGroupContent.ContentSequence).filter(codeMeaningEquals("Length"));
// Retrieve Length Measurement Data
return getLengthMeasurementData(lengthMeasurementContent, displaySets);
};
export default retrieveDataFromSR = (Part10SRArrayBuffer) => {
const allDisplaySets = getAllDisplaySets();
// get the dicom data as an Object
let dicomData = dcmjs.data.DicomMessage.readFile(Part10SRArrayBuffer);
let dataset = dcmjs.data.DicomMetaDictionary.naturalizeDataset(dicomData.dict);
// Convert the SR into the kind of object the Measurements package is expecting
return imagingMeasurementsToMeasurementData(dataset, allDisplaySets);
};

105
Packages/ohif-measurement-table/client/utils/srUtils.js Normal file
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@ -0,0 +1,105 @@
import { dcmjs } from 'meteor/ohif:cornerstone';
const supportedSopClassUIDs = ['1.2.840.10008.5.1.4.1.1.88.22'];
const toArray = function(x) {
return (x.constructor.name === "Array" ? x : [x]);
};
const codeMeaningEquals = (codeMeaningName) => {
return (contentItem) => {
return contentItem.ConceptNameCodeSequence.CodeMeaning === codeMeaningName;
};
};
const getAllDisplaySets = () => {
const allStudies = OHIF.viewer.Studies.all();
let allDisplaySets = [];
allStudies.forEach(study => {
allDisplaySets = allDisplaySets.concat(study.displaySets);
});
return allDisplaySets;
};
const getInstanceMetadata = (displaySets, sopInstanceUid) => {
let instance;
// Use Array.some so that this loop stops when the internal loop
// has found the correct instance
displaySets.some(displaySet => {
// Search the display set to find the instance metadata for
return displaySet.images.find(instanceMetadata => {
if (instanceMetadata._sopInstanceUID === sopInstanceUid) {
instance = instanceMetadata;
return true;
}
});
});
return instance;
};
const getLatestSRSeries = () => {
const allStudies = OHIF.viewer.StudyMetadataList.all();
let latestSeries;
allStudies.forEach(study => {
study.getSeries().forEach(series => {
const firstInstance = series.getFirstInstance();
const sopClassUid = firstInstance._instance.sopClassUid;
if (supportedSopClassUIDs.includes(sopClassUid)) {
if(!latestSeries) {
latestSeries = series;
} else if (series._data.seriesDate > latestSeries._data.seriesDate ||
(series._data.seriesDate === latestSeries._data.seriesDate && series._data.seriesTime > latestSeries._data.seriesTime)) {
latestSeries = series;
}
}
});
});
return latestSeries;
};
const stringToArray = (string) => {
return Uint8Array.from(Array.from(string).map(letter => letter.charCodeAt(0)))
};
const multipartEncode = (dataset, boundary) => {
const denaturalizedMetaheader = dcmjs.data.DicomMetaDictionary.denaturalizeDataset(dataset._meta);
const dicomDict = new dcmjs.data.DicomDict(denaturalizedMetaheader);
dicomDict.dict = dcmjs.data.DicomMetaDictionary.denaturalizeDataset(dataset);
const part10Buffer = dicomDict.write();
const header = `\r\n--${boundary}\r\nContent-Type: application/dicom\r\n\r\n`;
const footer = `\r\n--${boundary}--`;
headerArray = stringToArray(header);
contentArray = new Uint8Array(part10Buffer);
footerArray = stringToArray(footer);
const multipartArray = new Uint8Array(headerArray.length + contentArray.length + footerArray.length);
multipartArray.set(headerArray, 0);
multipartArray.set(contentArray, headerArray.length);
multipartArray.set(footerArray, headerArray.length + contentArray.length);
return(multipartArray.buffer);
};
export {
codeMeaningEquals,
getAllDisplaySets,
getInstanceMetadata,
getLatestSRSeries,
multipartEncode,
toArray
}

1
Packages/ohif-measurement-table/package.js
View File

@ -15,6 +15,7 @@ Package.onUse(function(api) {
api.use('ohif:cornerstone-settings');
api.use('ohif:viewerbase');
api.use('ohif:measurements');
api.use('ohif:wadoproxy');
api.mainModule('client/index.js', 'client');
});

17
Packages/ohif-measurements/client/components/measurementLightTable/measurementLightTableView/measurementLightTableView.html
View File

@ -9,4 +9,21 @@
{{/each}}
{{/each}}
{{/let}}
{{#if hasAnyMeasurement}}
<div class="report-area">
{{#if saveEnabled}}
{{#if hasUnsavedChanges}}
<div class="unsaved-changes-alert">
You have unsaved changes
</div>
{{/if}}
{{/if}}
{{#form (extend api=instance.api)}}
{{#button class='btn p-x-2' action='exportCSV'}}Export CSV{{/button}}
{{#if saveEnabled}}
{{#button class='btn p-x-2' action='save' disabled=(not hasUnsavedChanges)}}Save to Archive{{/button}}
{{/if}}
{{/form}}
</div>
{{/if}}
</template>

59
Packages/ohif-measurements/client/components/measurementLightTable/measurementLightTableView/measurementLightTableView.js
View File

@ -8,9 +8,68 @@ Template.measurementLightTableView.onCreated(() => {
instance.data.measurementGroups = new ReactiveVar();
instance.path = 'viewer.studyViewer.measurements';
instance.saveObserver = new Tracker.Dependency();
instance.api = {
save() {
const successHandler = () => {
OHIF.ui.unsavedChanges.clear(`${instance.path}.*`);
instance.saveObserver.changed();
};
// Display the error messages
const errorHandler = data => {
OHIF.ui.showDialog('dialogInfo', Object.assign({ class: 'themed' }, data));
};
const promise = instance.data.measurementApi.storeMeasurements();
promise.then(successHandler).catch(errorHandler);
OHIF.ui.showDialog('dialogLoading', {
promise,
text: 'Measurements saved.'
});
return promise;
},
exportCSV() {
const { measurementApi, timepointApi } = instance.data;
OHIF.measurements.exportCSV(measurementApi, timepointApi);
}
};
instance.autorun(() => {
measurementApi.changeObserver.depend();
const data = OHIF.measurements.getMeasurementsGroupedByNumber(measurementApi, timepointApi);
instance.data.measurementGroups.set(data);
});
});
Template.measurementLightTableView.helpers({
hasUnsavedChanges() {
const instance = Template.instance();
// Run this computation on save or every time any measurement / timepoint suffer changes
OHIF.ui.unsavedChanges.depend();
instance.saveObserver.depend();
return OHIF.ui.unsavedChanges.probe('viewer.*') !== 0;
},
hasAnyMeasurement() {
const instance = Template.instance();
const groups = instance.data.measurementGroups.get();
if (!groups) {
return false;
}
const group = groups.find(item => item.measurementRows.length > 0);
return group;
},
saveEnabled() {
const server = OHIF.servers.getCurrentServer();
return (server && server.type === 'dicomWeb');
}
});

6
Packages/ohif-measurements/client/components/measurementLightTable/measurementLightTableView/measurementLightTableView.styl
View File

@ -11,3 +11,9 @@
theme('background-color', '$activeColor')
theme('border', '1px solid $uiBorderColorActive')
color: #000
.unsaved-changes-alert
padding-bottom: 10px;
font-size: 11px;
color: #FF0;
font-weight: 100;

6
Packages/ohif-studies/imports/both/services/wado/retrieveMetadata.js
View File

@ -205,12 +205,6 @@ async function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
const seriesMap = {};
const seriesList = [];
if (!WADOProxy) {
WADOProxy = {
convertURL: (a => a)
};
}
if (!resultData.length) {
return;
}

6
Packages/ohif-studies/imports/client/lib/retrieveStudyMetadata.js
View File

@ -6,11 +6,13 @@ import 'meteor/ohif:viewerbase';
// promises and prevent unnecessary subsequent calls to the server
const StudyMetaDataPromises = new Map();
/**
* Delete the study promise cached to ensure next retrieve will get it retrieved by server call
* Delete the cached study metadata retrieval promise to ensure that the browser will
* re-retrieve the study metadata when it is next requested
*
* @param {String} studyInstanceUid The UID of the Study to be removed from cache
*
*
*/
OHIF.studies.deleteStudyMetadataPromise = (studyInstanceUid) => {
if (StudyMetaDataPromises.has(studyInstanceUid)) {

18
Packages/ohif-wadoproxy/both/convertURL.js Normal file
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@ -0,0 +1,18 @@
import queryString from 'query-string';
WADOProxy.convertURL = (url, serverConfiguration) => {
if (!url) {
return null;
}
if (serverConfiguration.requestOptions &&
serverConfiguration.requestOptions.requestFromBrowser === true) {
return url;
}
const { settings } = WADOProxy;
const serverId = serverConfiguration._id;
const query = queryString.stringify({url, serverId});
return `${settings.uri}?${query}`;
}

5
Packages/ohif-wadoproxy/server/initialize.js → Packages/ohif-wadoproxy/both/initialize.js
View File

@ -1,7 +1,6 @@
import { Meteor } from 'meteor/meteor';
import { OHIF } from 'meteor/ohif:core';
Settings = Object.assign({
WADOProxy.settings = Object.assign({
uri : OHIF.utils.absoluteUrl("/__wado_proxy"),
enabled: true
}, (Meteor.settings && Meteor.settings.proxy) ? Meteor.settings.proxy : {});
}, (Meteor.settings && Meteor.settings.proxy) ? Meteor.settings.proxy : {});

1
Packages/ohif-wadoproxy/both/namespace.js Executable file
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@ -0,0 +1 @@
WADOProxy = {};

10
Packages/ohif-wadoproxy/package.js
View File

@ -5,6 +5,7 @@ Package.describe({
});
Npm.depends({
'query-string': '5.1.1',
'performance-now': '2.1.0'
});
@ -12,17 +13,16 @@ Package.onUse(function(api) {
api.versionsFrom('1.4');
api.use('ecmascript');
api.use('standard-app-packages');
api.use('clinical:router@2.0.19');
api.use('ohif:core');
api.use('ohif:servers');
api.addFiles('server/namespace.js', 'server');
api.addFiles('server/initialize.js', 'server');
api.addFiles('both/namespace.js', ['client', 'server']);
api.addFiles('both/convertURL.js', ['client', 'server']);
api.addFiles('both/initialize.js', ['client', 'server']);
api.addFiles('server/routes.js', 'server');
api.addFiles('server/convertURL.js', 'server');
// Global exports
api.export('WADOProxy');
});

15
Packages/ohif-wadoproxy/server/convertURL.js
View File

@ -1,15 +0,0 @@
const querystring = require("querystring");
WADOProxy.convertURL = (url, serverConfiguration) => {
if (!Settings.enabled) {
return url;
}
if (!url) {
return null;
}
const serverId = serverConfiguration._id;
const query = querystring.stringify({url, serverId});
return `${Settings.uri}?${query}`;
}

1
Packages/ohif-wadoproxy/server/namespace.js
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@ -1 +0,0 @@
WADOProxy = {};

2
Packages/ohif-wadoproxy/server/routes.js
View File

@ -170,4 +170,4 @@ const handleRequest = function() {
// Setup a Route using Iron Router to avoid Cross-origin resource sharing
// (CORS) errors. We only handle this route on the Server.
Router.route(Settings.uri.replace(OHIF.utils.absoluteUrl(), ''), handleRequest, { where: 'server' });
Router.route(WADOProxy.settings.uri.replace(OHIF.utils.absoluteUrl(), ''), handleRequest, { where: 'server' });

4
StandaloneViewer/StandaloneViewer/client/components/viewer/viewer.js
View File

@ -3,7 +3,7 @@ import { Session } from 'meteor/session';
import { Tracker } from 'meteor/tracker';
import { ReactiveDict } from 'meteor/reactive-dict';
import { OHIF } from 'meteor/ohif:core';
import { MeasurementTable, measurementEvents } from 'meteor/ohif:measurement-table';
import { MeasurementTable } from 'meteor/ohif:measurement-table';
import 'meteor/ohif:viewerbase';
import 'meteor/ohif:metadata';
@ -133,7 +133,7 @@ Template.viewer.onRendered(function() {
Template.viewer.events( Object.assign({
// Viewer Events
},
measurementEvents
MeasurementTable.measurementEvents
));
Template.viewer.helpers({