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Updated Trial Criteria selection, added groundwork for allowing multiple criteria (LT-188)

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This commit is contained in:
Erik Ziegler 2016-03-07 13:36:48 +01:00
parent 9970b8795b
commit c4ad6b04b5
7 changed files with 175 additions and 133 deletions
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18
Packages/lesiontracker/client/components/irRCDescription/irRCDescription.html Normal file
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@ -0,0 +1,18 @@
<template name="irRCDescription">
<h4>irRC</h4>
<h5>Baseline Checks</h5>
<ul>
<li>Target lesions must be >= 10 X 10 mm AND >= double the acquisition slice thickness by CT and MR</li>
<li>Up to a max of 5 target lesions per organ</li>
<li>Up to a max of 10 target lesions total</li>
<li>Non-targets can only be assessed as 'present'</li>
<li>Target lesions must have measurements (cannot be assessed as CR, UN/NE, EX)</li>
</ul>
<h5>New Lesion Checks for Follow-ups</h5>
<ul>
<li>New target lesions must be >= 5 X 5 mm AND >= double the acquisition slice thickness by CT and MR</li>
<li>Up to a max of 5 target lesions per organ</li>
<li>Up to a max of 10 target lesions total</li>
</ul>
<!--Time Point Measurement Total = SPD target lesions + SPD new lesions (SPD = sum of product of long axis and short axis diameters)-->
</template>

69
Packages/lesiontracker/client/components/optionsModal/optionsModal.html
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@ -9,58 +9,23 @@
<div class="modal-body">
<div class="row">
<div class="col-md-12">
<h4>Select a Trial Criteria Type</h4>
<label for="recistCriteria" class="trialCriteriaLabel">
<input type="radio" name="trialCriteria" checked="true" id="recistCriteria" value='RECIST' class="trialCriteria"> RECIST 1.1
</label>
<label for="irRCCriteria" class="trialCriteriaLabel">
<input type="radio" name="trialCriteria" id="irRCCriteria" value='irRC' class="trialCriteria"> irRC
</label>
</div>
</div>
<br/>
<div class="row">
<div class="col-md-12">
<h4>Trial Criteria Descriptions</h4>
<ul class="nav nav-tabs" role="tablist">
<li role="presentation" class="active">
<a href="#RECISTDescription" aria-controls="home" role="tab" data-toggle="tab">RECIST 1.1</a>
</li>
<li role="presentation">
<a href="#irRCDescription" aria-controls="profile" role="tab" data-toggle="tab">irRC</a>
</li>
</ul>
<div class="tab-content">
<div role="tabpanel" class="tab-pane fade in active" id="RECISTDescription">
<h5>Baseline Checks</h5>
<ul>
<li>Extranodal lesions must be >= 10 mm long axis AND >= double the acquisition slice thickness by CT and MR</li>
<li>Extranodal lesions must be >= 20 mm on chest x-ray (although x-rays rarely used for clinical trial assessment)</li>
<li>Nodal lesions must be >= 15 mm short axis AND >= double the acquisition slice thickness by CT and MR</li>
<li>Up to a max of 2 target lesions per organ</li>
<li>Up to a max of 5 target lesions total</li>
<li>Non-targets can only be assessed as 'present'</li>
<li>Target lesions must have measurements (cannot be assessed as CR, UN/NE, EX)</li>
</ul>
<!-- Time Point Measurement Total = Sum of long axis measurements for extranodal target lesion + short axis measurements for nodal lesions</li>-->
</div>
<div role="tabpanel" class="tab-pane fade" id="irRCDescription">
<h5>Baseline Checks</h5>
<ul>
<li>Target lesions must be >= 10 X 10 mm AND >= double the acquisition slice thickness by CT and MR</li>
<li>Up to a max of 5 target lesions per organ</li>
<li>Up to a max of 10 target lesions total</li>
<li>Non-targets can only be assessed as 'present'</li>
<li>Target lesions must have measurements (cannot be assessed as CR, UN/NE, EX)</li>
</ul>
<h5>New Lesion Checks for Follow-ups</h5>
<ul>
<li>New target lesions must be >= 5 X 5 mm AND >= double the acquisition slice thickness by CT and MR</li>
<li>Up to a max of 5 target lesions per organ</li>
<li>Up to a max of 10 target lesions total</li>
</ul>
<!--Time Point Measurement Total = SPD target lesions + SPD new lesions (SPD = sum of product of long axis and short axis diameters)-->
</div>
<h3>Select one or more Trial Criteria types:</h3>
{{ #each trialCriteriaTypes}}
<label for="{{id}}Criteria" class="trialCriteriaLabel">
<!-- TODO: Change to checkbox for multiple criteria !-->
<input type="radio" name="trialCriteria" id="{{id}}Criteria" value='{{id}}' class="trialCriteria" checked={{selected}}>
{{name}}
</label>
{{ /each }}
<div>
<h3>Selected Trial Criteria:</h3>
{{ #each trialCriteriaTypes}}
{{ #if selected }}
<div class="trialCriteriaPanel panel fade in" id="{{id}}Description">
{{> Template.dynamic template=descriptionTemplate }}
</div>
{{ /if }}
{{ /each }}
</div>
</div>
</div>

46
Packages/lesiontracker/client/components/optionsModal/optionsModal.js
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@ -1,4 +1,24 @@
Session.setDefault('TrialResponseAssessmentCriteria', 'RECIST');
TrialCriteriaTypes = new Meteor.Collection(null);
TrialCriteriaTypes.insert({
id: 'RECIST',
name: 'RECIST 1.1',
descriptionTemplate: 'recistDescription',
selected: true
});
TrialCriteriaTypes.insert({
id: 'irRC',
name: 'irRC',
descriptionTemplate: 'irRCDescription',
selected: false
});
Template.optionsModal.helpers({
trialCriteriaTypes: function() {
return TrialCriteriaTypes.find();
}
});
Template.optionsModal.events({
/**
@ -8,16 +28,24 @@ Template.optionsModal.events({
* @param e The 'change' event on the selected radio button
*/
'change input.trialCriteria': function(e) {
// Get the Trial Criteria type that the selected radio button represents
var radioButton = $(e.currentTarget);
var criteriaType = radioButton.val();
var isChecked = e.currentTarget.checked;
// Set this as the current Trial Response Assessment Criteria
// TODO: Update when we have more trial-level support
// (Currently this information is stored in Session, later this will change)
Session.set('TrialResponseAssessmentCriteria', criteriaType);
// Set "Selected" to false for the entire collection
// TODO: Remove this when we allow multiple criteria
TrialCriteriaTypes.update({}, {
$set: {
selected: false
}
}, {
multi: true
});
log.info('Trial Criteria changed to: ' + criteriaType);
// Set the current Criteria in the collection to selected
TrialCriteriaTypes.update(this._id, {
$set: {
selected: isChecked
}
});
},
/**
* When the Clear Study/Timepoint Associations button is clicked, we

14
Packages/lesiontracker/client/components/recistDescription/recistDescription.html Normal file
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@ -0,0 +1,14 @@
<template name="recistDescription">
<h4>RECIST 1.1</h4>
<h5>Baseline Checks</h5>
<ul>
<li>Extranodal lesions must be >= 10 mm long axis AND >= double the acquisition slice thickness by CT and MR</li>
<li>Extranodal lesions must be >= 20 mm on chest x-ray (although x-rays rarely used for clinical trial assessment)</li>
<li>Nodal lesions must be >= 15 mm short axis AND >= double the acquisition slice thickness by CT and MR</li>
<li>Up to a max of 2 target lesions per organ</li>
<li>Up to a max of 5 target lesions total</li>
<li>Non-targets can only be assessed as 'present'</li>
<li>Target lesions must have measurements (cannot be assessed as CR, UN/NE, EX)</li>
</ul>
<!-- Time Point Measurement Total = Sum of long axis measurements for extranodal target lesion + short axis measurements for nodal lesions</li>-->
</template>

118
Packages/lesiontracker/lib/TrialCriteriaConstraints.js
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@ -321,70 +321,78 @@ function irRC(image) {
* Retrieve trial criteria constraints based on the image that measurements appear upon
* If no image is specified, it is assumed that group or per Organ level criteria are desired.
*
* @param criteriaType A valid Trial Criteria set name (e.g. 'RECIST' or 'irRC')
* @param criteriaTypes An array of valid Trial Criteria set names (e.g. ['RECIST', 'irRC'])
* NOTE: Multiple criteria are not yet supported
*
* @param imageId A Cornerstone Image ID
* @returns {*} An Object of Trial Criteria that can be used to validate measurements' conformance
*/
getTrialCriteriaConstraints = function(criteriaType, imageId) {
if (!TrialCriteriaConstraints[criteriaType]) {
throw 'No such Trial Criteria defined: ' + criteriaType;
}
getTrialCriteriaConstraints = function(criteriaTypes, imageId) {
// TODO: update this when we allow multiple criteria
var allCriteria = [];
criteriaTypes.forEach(function(criteriaType) {
if (!TrialCriteriaConstraints[criteriaType]) {
throw 'No such Trial Criteria defined: ' + criteriaType;
}
// If no imageId was specified, skip customization of the criteria
// and return the requested criteria right away
var criteria;
if (!imageId) {
criteria = TrialCriteriaConstraints[criteriaType]();
return criteria;
}
// If no imageId was specified, skip customization of the criteria
// and return the requested criteria right away
var criteria;
if (!imageId) {
criteria = TrialCriteriaConstraints[criteriaType]();
return criteria;
}
// Otherwise, retrieve the series metaData to identify the modality of the image
var seriesMetaData = cornerstoneTools.metaData.get('series', imageId);
if (!seriesMetaData) {
return;
}
// Otherwise, retrieve the series metaData to identify the modality of the image
var seriesMetaData = cornerstoneTools.metaData.get('series', imageId);
if (!seriesMetaData) {
return;
}
// TODO: Get the rest of the metaData that has already been loaded by Cornerstone
var image = {};
// TODO: Get the rest of the metaData that has already been loaded by Cornerstone
var image = {};
// If we are looking at an MR or CT image, we should pass the slice thickness
// to the Trial Criteria functions so that they can customize the validation rules
if (seriesMetaData.modality === 'MR' || seriesMetaData.modality === 'CT') {
var instanceMetaData = cornerstoneTools.metaData.get('instance', imageId);
image.acquisitionSliceThickness = instanceMetaData.sliceThickness;
}
// If we are looking at an MR or CT image, we should pass the slice thickness
// to the Trial Criteria functions so that they can customize the validation rules
if (seriesMetaData.modality === 'MR' || seriesMetaData.modality === 'CT') {
var instanceMetaData = cornerstoneTools.metaData.get('instance', imageId);
image.acquisitionSliceThickness = instanceMetaData.sliceThickness;
}
// Retrieve the study metaData in order to find the timepoint type
var studyMetaData = cornerstoneTools.metaData.get('study', imageId);
if (!studyMetaData) {
return;
}
// Retrieve the study metaData in order to find the timepoint type
var studyMetaData = cornerstoneTools.metaData.get('study', imageId);
if (!studyMetaData) {
return;
}
// Retrieve the Study document from the Collection of associated Studies
var study = Studies.findOne({
studyInstanceUid: studyMetaData.studyInstanceUid
// Retrieve the Study document from the Collection of associated Studies
var study = Studies.findOne({
studyInstanceUid: studyMetaData.studyInstanceUid
});
if (!study) {
return;
}
// Find the related Timepoint document
var timepoint = Timepoints.findOne({
timepointId: study.timepointId
});
if (!timepoint) {
log.warn('Timepoint related to study is missing.');
return;
}
// Retrieve the Timepoint's type (e.g. 'baseline' or 'followup')
var timepointType = timepoint.timepointType;
// Obtain the customized trial criteria given the image metaData
criteria = TrialCriteriaConstraints[criteriaType](image);
// Return the relevant criteria given the current timepoint type
allCriteria.push(criteria[timepointType]);
});
if (!study) {
return;
}
// Find the related Timepoint document
var timepoint = Timepoints.findOne({
timepointId: study.timepointId
});
if (!timepoint) {
log.warn('Timepoint related to study is missing.');
return;
}
// Retrieve the Timepoint's type (e.g. 'baseline' or 'followup')
var timepointType = timepoint.timepointType;
// Obtain the customized trial criteria given the image metaData
criteria = TrialCriteriaConstraints[criteriaType](image);
// Return the relevant criteria given the current timepoint type
return criteria[timepointType];
return allCriteria[0];
};

39
Packages/lesiontracker/lib/TrialResponseCriteria.js
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@ -70,13 +70,9 @@ function assessGroupOfMeasurements(constraints) {
type: type
});
// Get the criteria type so we can calculate total lesion burden
var criteriaType = Session.get('TrialResponseAssessmentCriteria');
// Calculate some simple group-level Measurement statistics for validation
var testStructure = {
totalNumberOfLesions: Measurements.find().count(),
totalLesionBurden: calculateTotalLesionBurden(criteriaType)
totalNumberOfLesions: Measurements.find().count()
};
// Run the conformance checks with the validate.js library
@ -220,8 +216,12 @@ function assessSingleMeasurement(constraints, measurementData) {
function validateSingleMeasurement(measurementData) {
// Obtain the name of the current TrialResponseAssessmentCriteria that
// we are using.
var criteriaType = Session.get('TrialResponseAssessmentCriteria');
var currentConstraints = getTrialCriteriaConstraints(criteriaType, measurementData.imageId);
var criteriaTypes = TrialCriteriaTypes.find({
selected: true
}).map(function(criteria) {
return criteria.id;
});
var currentConstraints = getTrialCriteriaConstraints(criteriaTypes, measurementData.imageId);
// If we have no relevant constraints, stop here
if (!currentConstraints) {
@ -264,12 +264,16 @@ function validateSingleMeasurement(measurementData) {
function validateGroups() {
log.info('validateGroups');
// Obtain the name of the current TrialResponseAssessmentCriteria that
// Obtain the names of the current TrialResponseAssessmentCriteria that
// we are using.
var criteriaType = Session.get('TrialResponseAssessmentCriteria');
var criteriaTypes = TrialCriteriaTypes.find({
selected: true
}).map(function(criteria) {
return criteria.id;
});
// Criteria for the specific image are retrieved from the general set of criteria.
var currentConstraints = getTrialCriteriaConstraints(criteriaType);
var currentConstraints = getTrialCriteriaConstraints(criteriaTypes);
if (!currentConstraints) {
return;
}
@ -297,10 +301,13 @@ function validateGroups() {
}
function validateAll() {
log.info('validateAll');
// Obtain the name of the current TrialResponseAssessmentCriteria that
// Obtain the names of the current TrialResponseAssessmentCriteria that
// we are using.
var criteriaType = Session.get('TrialResponseAssessmentCriteria');
var criteriaTypes = TrialCriteriaTypes.find({
selected: true
}).map(function(criteria) {
return criteria.id;
});
Measurements.find().forEach(function(measurement) {
Object.keys(measurement.timepoints).forEach(function(timepointId) {
@ -311,7 +318,7 @@ function validateAll() {
currentMeasurement._id = measurement._id;
// Criteria for the specific image are retrieved from the general set of criteria.
var currentConstraints = getTrialCriteriaConstraints(criteriaType, currentMeasurement.imageId);
var currentConstraints = getTrialCriteriaConstraints(criteriaTypes, currentMeasurement.imageId);
if (!currentConstraints) {
return;
}
@ -333,8 +340,6 @@ var validationTimeout = 400;
* @param measurementData Input measurement data from CornerstoneTools
*/
function validateDelayed(measurementData) {
log.info('validateAllDelayed');
// Erase any currently-waiting validation call
clearTimeout(validationTimeout);

4
Packages/lesiontracker/package.js
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@ -71,6 +71,9 @@ Package.onUse(function(api) {
api.addFiles('client/components/optionsModal/optionsModal.styl', 'client');
api.addFiles('client/components/optionsModal/optionsModal.js', 'client');
api.addFiles('client/components/recistDescription/recistDescription.html', 'client');
api.addFiles('client/components/irRCDescription/irRCDescription.html', 'client');
api.addFiles('client/components/lesionLocationDialog/lesionLocationDialog.html', 'client');
api.addFiles('client/components/lesionLocationDialog/lesionLocationDialog.js', 'client');
api.addFiles('client/components/lesionLocationDialog/lesionLocationDialog.styl', 'client');
@ -201,6 +204,7 @@ Package.onUse(function(api) {
api.export('ValidationErrors', 'client');
api.export('LesionLocations', 'client');
api.export('LocationResponses', 'client');
api.export('TrialCriteriaTypes', 'client');
// Export collections spanning both client and server
api.export('ImageMeasurements', [ 'client', 'server' ]);