Updated Trial Criteria selection, added groundwork for allowing multiple criteria (LT-188)
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Erik Ziegler committed
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@@ -321,70 +321,78 @@ function irRC(image) {
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* Retrieve trial criteria constraints based on the image that measurements appear upon
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* If no image is specified, it is assumed that group or per Organ level criteria are desired.
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*
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* @param criteriaType A valid Trial Criteria set name (e.g. 'RECIST' or 'irRC')
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* @param criteriaTypes An array of valid Trial Criteria set names (e.g. ['RECIST', 'irRC'])
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* NOTE: Multiple criteria are not yet supported
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*
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* @param imageId A Cornerstone Image ID
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* @returns {*} An Object of Trial Criteria that can be used to validate measurements' conformance
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*/
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getTrialCriteriaConstraints = function(criteriaType, imageId) {
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if (!TrialCriteriaConstraints[criteriaType]) {
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throw 'No such Trial Criteria defined: ' + criteriaType;
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}
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getTrialCriteriaConstraints = function(criteriaTypes, imageId) {
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// TODO: update this when we allow multiple criteria
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var allCriteria = [];
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criteriaTypes.forEach(function(criteriaType) {
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if (!TrialCriteriaConstraints[criteriaType]) {
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throw 'No such Trial Criteria defined: ' + criteriaType;
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}
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// If no imageId was specified, skip customization of the criteria
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// and return the requested criteria right away
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var criteria;
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if (!imageId) {
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criteria = TrialCriteriaConstraints[criteriaType]();
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return criteria;
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}
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// If no imageId was specified, skip customization of the criteria
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// and return the requested criteria right away
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var criteria;
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if (!imageId) {
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criteria = TrialCriteriaConstraints[criteriaType]();
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return criteria;
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}
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// Otherwise, retrieve the series metaData to identify the modality of the image
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var seriesMetaData = cornerstoneTools.metaData.get('series', imageId);
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if (!seriesMetaData) {
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return;
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}
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// Otherwise, retrieve the series metaData to identify the modality of the image
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var seriesMetaData = cornerstoneTools.metaData.get('series', imageId);
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if (!seriesMetaData) {
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return;
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}
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// TODO: Get the rest of the metaData that has already been loaded by Cornerstone
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var image = {};
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// TODO: Get the rest of the metaData that has already been loaded by Cornerstone
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var image = {};
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// If we are looking at an MR or CT image, we should pass the slice thickness
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// to the Trial Criteria functions so that they can customize the validation rules
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if (seriesMetaData.modality === 'MR' || seriesMetaData.modality === 'CT') {
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var instanceMetaData = cornerstoneTools.metaData.get('instance', imageId);
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image.acquisitionSliceThickness = instanceMetaData.sliceThickness;
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}
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// If we are looking at an MR or CT image, we should pass the slice thickness
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// to the Trial Criteria functions so that they can customize the validation rules
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if (seriesMetaData.modality === 'MR' || seriesMetaData.modality === 'CT') {
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var instanceMetaData = cornerstoneTools.metaData.get('instance', imageId);
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image.acquisitionSliceThickness = instanceMetaData.sliceThickness;
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}
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// Retrieve the study metaData in order to find the timepoint type
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var studyMetaData = cornerstoneTools.metaData.get('study', imageId);
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if (!studyMetaData) {
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return;
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}
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// Retrieve the study metaData in order to find the timepoint type
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var studyMetaData = cornerstoneTools.metaData.get('study', imageId);
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if (!studyMetaData) {
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return;
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}
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// Retrieve the Study document from the Collection of associated Studies
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var study = Studies.findOne({
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studyInstanceUid: studyMetaData.studyInstanceUid
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// Retrieve the Study document from the Collection of associated Studies
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var study = Studies.findOne({
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studyInstanceUid: studyMetaData.studyInstanceUid
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});
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if (!study) {
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return;
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}
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// Find the related Timepoint document
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var timepoint = Timepoints.findOne({
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timepointId: study.timepointId
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});
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if (!timepoint) {
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log.warn('Timepoint related to study is missing.');
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return;
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}
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// Retrieve the Timepoint's type (e.g. 'baseline' or 'followup')
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var timepointType = timepoint.timepointType;
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// Obtain the customized trial criteria given the image metaData
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criteria = TrialCriteriaConstraints[criteriaType](image);
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// Return the relevant criteria given the current timepoint type
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allCriteria.push(criteria[timepointType]);
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});
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if (!study) {
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return;
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}
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// Find the related Timepoint document
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var timepoint = Timepoints.findOne({
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timepointId: study.timepointId
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});
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if (!timepoint) {
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log.warn('Timepoint related to study is missing.');
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return;
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}
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// Retrieve the Timepoint's type (e.g. 'baseline' or 'followup')
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var timepointType = timepoint.timepointType;
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// Obtain the customized trial criteria given the image metaData
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criteria = TrialCriteriaConstraints[criteriaType](image);
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// Return the relevant criteria given the current timepoint type
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return criteria[timepointType];
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return allCriteria[0];
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};
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@@ -70,13 +70,9 @@ function assessGroupOfMeasurements(constraints) {
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type: type
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});
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// Get the criteria type so we can calculate total lesion burden
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var criteriaType = Session.get('TrialResponseAssessmentCriteria');
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// Calculate some simple group-level Measurement statistics for validation
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var testStructure = {
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totalNumberOfLesions: Measurements.find().count(),
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totalLesionBurden: calculateTotalLesionBurden(criteriaType)
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totalNumberOfLesions: Measurements.find().count()
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};
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// Run the conformance checks with the validate.js library
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@@ -220,8 +216,12 @@ function assessSingleMeasurement(constraints, measurementData) {
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function validateSingleMeasurement(measurementData) {
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// Obtain the name of the current TrialResponseAssessmentCriteria that
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// we are using.
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var criteriaType = Session.get('TrialResponseAssessmentCriteria');
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var currentConstraints = getTrialCriteriaConstraints(criteriaType, measurementData.imageId);
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var criteriaTypes = TrialCriteriaTypes.find({
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selected: true
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}).map(function(criteria) {
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return criteria.id;
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});
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var currentConstraints = getTrialCriteriaConstraints(criteriaTypes, measurementData.imageId);
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// If we have no relevant constraints, stop here
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if (!currentConstraints) {
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@@ -264,12 +264,16 @@ function validateSingleMeasurement(measurementData) {
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function validateGroups() {
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log.info('validateGroups');
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// Obtain the name of the current TrialResponseAssessmentCriteria that
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// Obtain the names of the current TrialResponseAssessmentCriteria that
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// we are using.
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var criteriaType = Session.get('TrialResponseAssessmentCriteria');
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var criteriaTypes = TrialCriteriaTypes.find({
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selected: true
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}).map(function(criteria) {
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return criteria.id;
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});
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// Criteria for the specific image are retrieved from the general set of criteria.
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var currentConstraints = getTrialCriteriaConstraints(criteriaType);
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var currentConstraints = getTrialCriteriaConstraints(criteriaTypes);
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if (!currentConstraints) {
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return;
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}
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@@ -297,10 +301,13 @@ function validateGroups() {
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}
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function validateAll() {
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log.info('validateAll');
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// Obtain the name of the current TrialResponseAssessmentCriteria that
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// Obtain the names of the current TrialResponseAssessmentCriteria that
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// we are using.
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var criteriaType = Session.get('TrialResponseAssessmentCriteria');
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var criteriaTypes = TrialCriteriaTypes.find({
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selected: true
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}).map(function(criteria) {
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return criteria.id;
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});
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Measurements.find().forEach(function(measurement) {
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Object.keys(measurement.timepoints).forEach(function(timepointId) {
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@@ -311,7 +318,7 @@ function validateAll() {
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currentMeasurement._id = measurement._id;
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// Criteria for the specific image are retrieved from the general set of criteria.
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var currentConstraints = getTrialCriteriaConstraints(criteriaType, currentMeasurement.imageId);
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var currentConstraints = getTrialCriteriaConstraints(criteriaTypes, currentMeasurement.imageId);
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if (!currentConstraints) {
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return;
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}
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@@ -333,8 +340,6 @@ var validationTimeout = 400;
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* @param measurementData Input measurement data from CornerstoneTools
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*/
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function validateDelayed(measurementData) {
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log.info('validateAllDelayed');
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// Erase any currently-waiting validation call
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clearTimeout(validationTimeout);
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