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Fixing metadata issues

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This commit is contained in:
Bruno Alves de Faria 2017-02-22 08:00:00 -03:00
parent a742c8036d
commit 19c31ffbb8
14 changed files with 197 additions and 128 deletions
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2
LesionTracker/client/components/viewer/viewer.js
View File

@ -86,8 +86,6 @@ Template.viewer.onCreated(() => {
instance.data.studies.forEach(study => {
study.selected = true;
const studyMetadata = new OHIF.metadata.StudyMetadata(study);
study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
OHIF.viewer.Studies.insert(study);
});

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

@ -32,7 +32,7 @@ Meteor.startup(() => {
};
OHIF.viewer.stackImagePositionOffsetSynchronizer = new OHIF.viewerbase.StackImagePositionOffsetSynchronizer();
// Create the synchronizer used to update reference lines
OHIF.viewer.updateImageSynchronizer = new cornerstoneTools.Synchronizer('CornerstoneNewImage', cornerstoneTools.updateImageSynchronizer);
@ -77,8 +77,6 @@ Template.viewer.onCreated(() => {
ViewerData[contentId].studyInstanceUids = [];
instance.data.studies.forEach(study => {
study.selected = true;
const studyMetadata = new OHIF.metadata.StudyMetadata(study);
study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
OHIF.viewer.Studies.insert(study);
ViewerData[contentId].studyInstanceUids.push(study.studyInstanceUid);
});

13
Packages/ohif-cornerstone/client/lib/classes/MetadataProvider.js
View File

@ -3,7 +3,7 @@ import { parsingUtils } from '../parsingUtils';
export class MetadataProvider {
constructor() {
this.metadataLookup = {};
this.metadataLookup = new Map();
}
/**
@ -58,7 +58,7 @@ export class MetadataProvider {
metadata.imagePlane = this.getImagePlane(instanceMetadata);
// Add the metadata to the imageId lookup object
this.metadataLookup[imageId] = metadata;
this.metadataLookup.set(imageId, metadata);
}
/**
@ -67,7 +67,7 @@ export class MetadataProvider {
* @returns image metadata
*/
getMetadata(imageId) {
return this.metadataLookup[imageId];
return this.metadataLookup.get(imageId);
}
/**
@ -82,7 +82,8 @@ export class MetadataProvider {
const metadata = {};
metadata[type] = data;
this.metadataLookup[imageId] = $.extend(this.metadataLookup[imageId], metadata);
const oldMetadata = this.metadataLookup.get(imageId);
this.metadataLookup.set(imageId, Object.assign(oldMetadata, metadata));
}
getFromDataSet(dataSet, type, tag) {
@ -104,7 +105,7 @@ export class MetadataProvider {
* @param image
*/
updateMetadata(image) {
const imageMetadata = this.metadataLookup[image.imageId];
const imageMetadata = this.metadataLookup.get(image.imageId);
if (!imageMetadata) {
return;
}
@ -252,7 +253,7 @@ export class MetadataProvider {
* @returns {Object} Relevant metadata of the specified type
*/
provider(type, imageId) {
const imageMetadata = this.metadataLookup[imageId];
const imageMetadata = this.metadataLookup.get(imageId);
if (!imageMetadata) {
return;
}

3
Packages/ohif-hanging-protocols/client/protocolEngine.js
View File

@ -407,9 +407,8 @@ HP.ProtocolEngine = class ProtocolEngine {
});
if (!alreadyLoaded) {
getStudyMetadata(priorStudy.studyInstanceUid, study => {
OHIF.studylist.retrieveStudyMetadata(priorStudy.studyInstanceUid).then(study => {
study.abstractPriorValue = abstractPriorValue;
study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(study);
OHIF.viewer.Studies.insert(study);
this.studies.push(study);
this.matchImages(viewport);

116
Packages/ohif-measurements/client/conformance/ConformanceCriteria.js
View File

@ -29,31 +29,36 @@ class ConformanceCriteria {
}
validate(trialCriteriaType) {
const baselineData = this.getData('baseline');
const followupData = this.getData('followup');
const mergedData = {
targets: [],
nonTargets: []
};
return new Promise((resolve, reject) => {
const baselinePromise = this.getData('baseline');
const followupPromise = this.getData('followup');
Promise.all([baselinePromise, followupPromise]).then(values => {
const [baselineData, followupData] = values;
const mergedData = {
targets: [],
nonTargets: []
};
mergedData.targets = mergedData.targets.concat(baselineData.targets);
mergedData.targets = mergedData.targets.concat(followupData.targets);
mergedData.nonTargets = mergedData.nonTargets.concat(baselineData.nonTargets);
mergedData.nonTargets = mergedData.nonTargets.concat(followupData.nonTargets);
mergedData.targets = mergedData.targets.concat(baselineData.targets);
mergedData.targets = mergedData.targets.concat(followupData.targets);
mergedData.nonTargets = mergedData.nonTargets.concat(baselineData.nonTargets);
mergedData.nonTargets = mergedData.nonTargets.concat(followupData.nonTargets);
this.maxTargets.set(null);
const resultBoth = this.validateTimepoint('both', trialCriteriaType, mergedData);
const resultBaseline = this.validateTimepoint('baseline', trialCriteriaType, baselineData);
const resultFollowup = this.validateTimepoint('followup', trialCriteriaType, followupData);
const nonconformities = resultBaseline.concat(resultFollowup).concat(resultBoth);
const groupedNonConformities = this.groupNonConformities(nonconformities);
this.maxTargets.set(null);
const resultBoth = this.validateTimepoint('both', trialCriteriaType, mergedData);
const resultBaseline = this.validateTimepoint('baseline', trialCriteriaType, baselineData);
const resultFollowup = this.validateTimepoint('followup', trialCriteriaType, followupData);
const nonconformities = resultBaseline.concat(resultFollowup).concat(resultBoth);
const groupedNonConformities = this.groupNonConformities(nonconformities);
// Keep both? Group the data only on viewer/measurementTable views?
// Work with not grouped data (worse lookup performance on measurementTableRow)?
this.nonconformities.set(nonconformities);
this.groupedNonConformities.set(groupedNonConformities);
// Keep both? Group the data only on viewer/measurementTable views?
// Work with not grouped data (worse lookup performance on measurementTableRow)?
this.nonconformities.set(nonconformities);
this.groupedNonConformities.set(groupedNonConformities);
return nonconformities;
resolve(nonconformities);
});
});
}
groupNonConformities(nonconformities) {
@ -128,48 +133,47 @@ class ConformanceCriteria {
* Build the data that will be used to do the conformance criteria checks
*/
getData(timepointType) {
const data = {
targets: [],
nonTargets: []
};
return new Promise((resolve, reject) => {
const data = {
targets: [],
nonTargets: []
};
const fillData = measurementType => {
const measurements = this.measurementApi.fetch(measurementType);
const studyPromises = [];
measurements.forEach(measurement => {
const { studyInstanceUid, imageId } = measurement;
const metadata = this.getImageInstanceMetadata(studyInstanceUid, imageId);
const timepointId = measurement.timepointId;
const timepoint = timepointId && this.timepointApi.timepoints.findOne({ timepointId });
const fillData = measurementType => {
const measurements = this.measurementApi.fetch(measurementType);
if (!timepoint || ((timepointType !== 'both') && (timepoint.timepointType !== timepointType))) {
return;
}
measurements.forEach(measurement => {
const { studyInstanceUid, imageId } = measurement;
data[measurementType].push({
measurement,
metadata,
timepoint
const timepointId = measurement.timepointId;
const timepoint = timepointId && this.timepointApi.timepoints.findOne({ timepointId });
if (!timepoint || ((timepointType !== 'both') && (timepoint.timepointType !== timepointType))) {
return;
}
const promise = OHIF.studylist.retrieveStudyMetadata(studyInstanceUid);
promise.then(study => {
const metadata = OHIF.viewer.metadataProvider.getMetadata(imageId);
data[measurementType].push({
measurement,
metadata: metadata.instance,
timepoint
});
});
studyPromises.push(promise);
});
});
};
};
fillData('targets');
fillData('nonTargets');
fillData('targets');
fillData('nonTargets');
return data;
}
getImageInstanceMetadata(studyInstanceUid, imageId) {
const study = OHIF.viewer.Studies.findBy({ studyInstanceUid });
// Stop here if the study was not found
if (!study) {
return;
}
const metadata = OHIF.cornerstone.metadataProvider.getMetadata(imageId);
return metadata ? metadata.instance : undefined;
Promise.all(studyPromises).then(() => {
resolve(data);
}).catch(reject);
});
}
}

21
Packages/ohif-measurements/client/lib/jumpToRowItem.js
View File

@ -21,7 +21,7 @@ function findAndRenderDisplaySet(displaySets, viewportIndex, studyInstanceUid, s
currentImageIdIndex: specificImageIndex
};
// Add a renderedCallback to activate the measurements once it's
// Add a renderedCallback to activate the measurements once it's
if (renderedCallback) {
displaySetData.renderedCallback = renderedCallback;
}
@ -45,20 +45,19 @@ function renderIntoViewport(viewportIndex, studyInstanceUid, seriesInstanceUid,
const element = $viewports.get(viewportIndex);
const startLoadingHandler = cornerstoneTools.loadHandlerManager.getStartLoadHandler();
startLoadingHandler(element);
getStudyMetadata(studyInstanceUid, loadedStudy => {
loadedStudy.displaySets = createStacks(loadedStudy);
OHIF.studylist.retrieveStudyMetadata(studyInstanceUid).then(study => {
OHIF.log.warn('renderIntoViewport');
// Double check to make sure this study wasn't already inserted
// into OHIF.viewer.Studies, so we don't cause duplicate entry errors
const loaded = OHIF.viewer.Studies.findBy({
studyInstanceUid: loadedStudy.studyInstanceUid
studyInstanceUid: study.studyInstanceUid
});
if (!loaded) {
OHIF.viewer.Studies.insert(loadedStudy);
OHIF.viewer.Studies.insert(study);
}
findAndRenderDisplaySet(loadedStudy.displaySets, viewportIndex, studyInstanceUid, seriesInstanceUid, sopInstanceUid, renderedCallback)
findAndRenderDisplaySet(study.displaySets, viewportIndex, studyInstanceUid, seriesInstanceUid, sopInstanceUid, renderedCallback);
});
}
}
@ -93,16 +92,16 @@ OHIF.measurements.jumpToRowItem = (rowItem, timepoints) => {
const $viewports = $('.imageViewerViewport');
const numViewports = Math.max($viewports.length, 1);
/*
/*
Two Timepoints, Two measurements, load Followup (FU and BA), display FU in left and BA in right
Two Timepoints, One measurement (BA), on 2x1 view: Display BA in right
Two Timepoints, One measurement (FU), on 2x1 view: Display FU in left
Two Timepoints, Two measurements, load Baseline (FU and BA) on 1x1 view: Display whichever is clicked on?
Two Timepoints, Two measurements, load Baseline (FU and BA) on 1x1 view: Display whichever is clicked on?
One Timepoint, One measurement: Display clicked on in 1x1
*/
const numViewportsToUpdate = Math.min(numTimepoints, numViewports);
for (var i=0; i < numViewportsToUpdate; i++) {
const timepoint = timepoints[i];
const timepointId = timepoint.timepointId;
@ -123,7 +122,7 @@ OHIF.measurements.jumpToRowItem = (rowItem, timepoints) => {
// or maybe just remove the 'error' this throws?
let enabledElement;
try {
enabledElement = cornerstone.getEnabledElement(element)
enabledElement = cornerstone.getEnabledElement(element)
} catch(error) {
OHIF.log.warn(error);
}
@ -135,7 +134,7 @@ OHIF.measurements.jumpToRowItem = (rowItem, timepoints) => {
if (series.seriesInstanceUid === measurementData.seriesInstanceUid &&
study.studyInstanceUid === measurementData.studyInstanceUid) {
// If it is, activate the measurements in this viewport and stop here
activateMeasurements(element, measurementData);
continue;

10
Packages/ohif-study-list/client/components/seriesDetailsModal/seriesDetailsTable/seriesDetailsTable.js
View File

@ -1,3 +1,8 @@
import { Template } from 'meteor/templating';
import { ReactiveDict } from 'meteor/reactive-dict';
import { _ } from 'meteor/underscore';
import { OHIF } from 'meteor/ohif:core';
Template.seriesDetailsTable.onCreated(() => {
const instance = Template.instance();
@ -31,8 +36,7 @@ Template.seriesDetailsTable.onRendered(() => {
// Get series list for the study
_.map(studies, (selectedStudy, index) => {
studies[index].seriesList = [];
getStudyMetadata(selectedStudy.studyInstanceUid, study => {
OHIF.studylist.retrieveStudyMetadata(study => {
// Set series list
studies[index].seriesList = study.seriesList;
studies[index].displaySeriesLoadingText = false;
@ -48,4 +52,4 @@ Template.seriesDetailsTable.helpers({
const instance = Template.instance();
return instance.selectedStudies.get('studies');
}
});
});

22
Packages/ohif-study-list/client/lib/getStudiesMetadata.js
View File

@ -1,10 +1,9 @@
import { $ } from 'meteor/jquery';
import { OHIF } from 'meteor/ohif:core';
/**
* Retrieves metaData for multiple studies at once.
*
* This function calls getStudyMetadata several times, asynchronously,
* This function calls retrieveStudyMetadata several times, asynchronously,
* and waits for all of the results to be returned.
*
* @param studyInstanceUids The UIDs of the Studies to be retrieved
@ -27,32 +26,21 @@ OHIF.studylist.getStudiesMetadata = (studyInstanceUids, doneCallback, failCallba
// Loop through the array of studyInstanceUids
studyInstanceUids.forEach(function(studyInstanceUid) {
// Create a new Deferred to monitor the progress of the asynchronous
// metaData retrieval
const deferred = new $.Deferred();
// Send the call, and attach doneCallbacks and failCallbacks
// which can resolve or reject the related promise based on its outcome
getStudyMetadata(studyInstanceUid, function(study) {
deferred.resolve(study);
}, function(error) {
deferred.reject(error);
});
const promise = OHIF.studylist.retrieveStudyMetadata(studyInstanceUid);
// Add the current promise to the array of promises
promises.push(deferred.promise());
promises.push(promise);
});
// When all of the promises are complete, this callback runs
$.when.apply($, promises).done(function() {
// Convert the Arguments Array-like Object to an actual array
const studies = $.makeArray(arguments);
Promise.all(promises).then(studies => {
// Pass the studies array to the doneCallback, if one exists
if (doneCallback && typeof doneCallback === 'function') {
doneCallback(studies);
}
}).fail(function(error) {
}).catch(error => {
OHIF.log.warn(error);
if (failCallback && typeof failCallback === 'function') {
failCallback(error);

1
Packages/ohif-study-list/client/lib/getStudyMetadata.js
View File

@ -1,6 +1,7 @@
import { OHIF } from 'meteor/ohif:core';
import 'meteor/ohif:viewerbase';
// DEPRECATED - use OHIF.studylist.retrieveStudyMetadata instead
// Define the StudyMetaData object. This is used as a cache
// to store study meta data information to prevent unnecessary
// calls to the server

1
Packages/ohif-study-list/client/lib/index.js
View File

@ -7,5 +7,6 @@ import './getStudiesMetadata.js';
import './importStudies.js';
import './openNewTab.js';
import './queryStudies.js';
import './retrieveStudyMetadata.js';
import './studylist.js';
import './switchToTab.js';

37
Packages/ohif-study-list/client/lib/queryStudies.js
View File

@ -5,31 +5,26 @@ import { OHIF } from 'meteor/ohif:core';
* @param studiesToQuery Studies to query
*/
queryStudies = function(studiesToQuery, options) {
const studiesQueried = [],
numberOfStudiesToQuery = studiesToQuery.length,
notify = (options || {}).notify || function() { /* noop */ }
let studiesQueried = 0;
const numberOfStudiesToQuery = studiesToQuery.length;
const notify = (options || {}).notify || function() { /* noop */ };
return new Promise((resolve, reject) => {
if (studiesToQuery.length < 1) {
return reject();
}
const promises = [];
studiesToQuery.forEach(function(studyToQuery) {
getStudyMetadata(studyToQuery.studyInstanceUid, function(study) {
studiesQueried.push(study);
notify({
total: numberOfStudiesToQuery,
processed: studiesQueried.length
});
if (studiesQueried.length === numberOfStudiesToQuery) {
resolve(studiesQueried);
}
studiesToQuery.forEach(studyToQuery => {
const promise = OHIF.studylist.retrieveStudyMetadata(studyToQuery.studyInstanceUid);
promise.then(study => {
studiesQueried++;
notify({
total: numberOfStudiesToQuery,
processed: studiesQueried
});
});
promises.push(promise);
});
}
return Promise.all(promises);
};
queryStudiesWithProgress = function(studiesToQuery) {
return OHIF.ui.showDialog('dialogProgress', {
@ -60,7 +55,7 @@ queryStudiesWithProgress = function(studiesToQuery) {
* @returns {number}
*/
getNumberOfFilesInStudy = function(study) {
var numberOFFilesToExport = 0;
let numberOFFilesToExport = 0;
study.seriesList.forEach(function(series) {
series.instances.forEach(function(instance) {

85
Packages/ohif-study-list/client/lib/retrieveStudyMetadata.js Normal file
View File

@ -0,0 +1,85 @@
import { Meteor } from 'meteor/meteor';
import { OHIF } from 'meteor/ohif:core';
import 'meteor/ohif:viewerbase';
// Define the StudyMetaDataPromises object. This is used as a cache to store study meta data
// promises and prevent unnecessary subsequent calls to the server
const StudyMetaDataPromises = new Map();
/**
* Retrieves study metadata using a server call
*
* @param {String} studyInstanceUid The UID of the Study to be retrieved
* @returns {Promise} that will be resolved with the metadata or rejected with the error
*/
OHIF.studylist.retrieveStudyMetadata = studyInstanceUid => {
// If the StudyMetaDataPromises cache already has a pending or resolved promise related to the
// given studyInstanceUid, then that promise is returned
if (StudyMetaDataPromises.has(studyInstanceUid)) {
return StudyMetaDataPromises.get(studyInstanceUid);
}
console.time('retrieveStudyMetadata');
// Create a promise to handle the data retrieval
const promise = new Promise((resolve, reject) => {
// If no study metadata is in the cache variable, we need to retrieve it from
// the server with a call.
Meteor.call('GetStudyMetadata', studyInstanceUid, function(error, study) {
console.timeEnd('retrieveStudyMetadata');
if (Meteor.user && Meteor.user()) {
HipaaLogger.logEvent({
eventType: 'viewed',
userId: Meteor.userId(),
userName: Meteor.user().profile.fullName,
collectionName: 'Study',
recordId: studyInstanceUid,
patientId: study.patientId,
patientName: study.patientName
});
}
if (error) {
OHIF.log.warn(error);
reject(error);
return;
}
if (!study) {
throw new Meteor.Error('GetStudyMetadata', 'No study data returned from server');
}
// Once the data was retrieved, the series are sorted by series and instance number
OHIF.viewerbase.sortStudy(study);
// Add additional metadata to our study from the studylist
const studylistStudy = StudyListStudies.findOne({
studyInstanceUid: study.studyInstanceUid
});
if (!studylistStudy) {
// return;
} else {
Object.assign(study, studylistStudy);
}
// Transform the study in a StudyMetadata object
const studyMetadata = new OHIF.metadata.StudyMetadata(study);
// Add the display sets to the study
study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
study.displaySets.forEach(displaySet => {
OHIF.viewerbase.stackManager.makeAndAddStack(study, displaySet);
});
// Resolve the promise with the final study metadata object
resolve(study);
});
});
// Store the promise in cache
StudyMetaDataPromises.set(studyInstanceUid, promise);
return promise;
};

6
Packages/ohif-viewerbase/client/components/viewer/studyTimepointBrowser/studyTimepointStudy.js
View File

@ -110,13 +110,11 @@ Template.studyTimepointStudy.events({
if (!alreadyLoaded) {
const $studies = instance.getStudyElement(true);
$studies.trigger('loadStarted');
getStudyMetadata(studyInstanceUid, study => {
const studyMetadata = new OHIF.metadata.StudyMetadata(study);
study.displaySets = sortingManager.getDisplaySets(studyMetadata);
OHIF.studylist.retrieveStudyMetadata(studyInstanceUid).then(study => {
instance.data.study = study;
OHIF.viewer.Studies.insert(study);
Meteor.setTimeout(() => {
Meteor.setTimeout(() => {
$studies.trigger('loadEnded');
instance.select(isQuickSwitch);
}, 1);

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

@ -52,8 +52,6 @@ Template.viewer.onCreated(() => {
ViewerData[contentId].studyInstanceUids = [];
instance.data.studies.forEach(study => {
study.selected = true;
const studyMetadata = new OHIF.metadata.StudyMetadata(study);
study.displaySets = OHIF.viewerbase.sortingManager.getDisplaySets(studyMetadata);
OHIF.viewer.Studies.insert(study);
ViewerData[contentId].studyInstanceUids.push(study.studyInstanceUid);
});
@ -67,4 +65,4 @@ Template.viewer.events({
const current = instance.data.state.get('leftSidebar');
instance.data.state.set('leftSidebar', !current);
}
});
});