From c4ad6b04b59349ef200b4d11b013088e8cc3dcdf Mon Sep 17 00:00:00 2001 From: Erik Ziegler Date: Mon, 7 Mar 2016 13:36:48 +0100 Subject: [PATCH] Updated Trial Criteria selection, added groundwork for allowing multiple criteria (LT-188) --- .../irRCDescription/irRCDescription.html | 18 +++ .../components/optionsModal/optionsModal.html | 69 +++------- .../components/optionsModal/optionsModal.js | 46 +++++-- .../recistDescription/recistDescription.html | 14 +++ .../lib/TrialCriteriaConstraints.js | 118 ++++++++++-------- .../lib/TrialResponseCriteria.js | 39 +++--- Packages/lesiontracker/package.js | 4 + 7 files changed, 175 insertions(+), 133 deletions(-) create mode 100644 Packages/lesiontracker/client/components/irRCDescription/irRCDescription.html create mode 100644 Packages/lesiontracker/client/components/recistDescription/recistDescription.html diff --git a/Packages/lesiontracker/client/components/irRCDescription/irRCDescription.html b/Packages/lesiontracker/client/components/irRCDescription/irRCDescription.html new file mode 100644 index 000000000..61c469a7f --- /dev/null +++ b/Packages/lesiontracker/client/components/irRCDescription/irRCDescription.html @@ -0,0 +1,18 @@ + \ No newline at end of file diff --git a/Packages/lesiontracker/client/components/optionsModal/optionsModal.html b/Packages/lesiontracker/client/components/optionsModal/optionsModal.html index f8335ef9b..01ea2a6ad 100644 --- a/Packages/lesiontracker/client/components/optionsModal/optionsModal.html +++ b/Packages/lesiontracker/client/components/optionsModal/optionsModal.html @@ -9,58 +9,23 @@
-

Select a Trial Criteria Type

- - -
-
-
-
-
-

Trial Criteria Descriptions

- -
-
-
Baseline Checks
-
    -
  • Extranodal lesions must be >= 10 mm long axis AND >= double the acquisition slice thickness by CT and MR
    • -
  • Extranodal lesions must be >= 20 mm on chest x-ray (although x-rays rarely used for clinical trial assessment)
    • -
  • Nodal lesions must be >= 15 mm short axis AND >= double the acquisition slice thickness by CT and MR
    • -
  • Up to a max of 2 target lesions per organ
    • -
  • Up to a max of 5 target lesions total
    • -
  • Non-targets can only be assessed as 'present'
    • -
  • Target lesions must have measurements (cannot be assessed as CR, UN/NE, EX)
    • -
- -
-
-
Baseline Checks
-
    -
  • Target lesions must be >= 10 X 10 mm AND >= double the acquisition slice thickness by CT and MR
    • -
  • Up to a max of 5 target lesions per organ
    • -
  • Up to a max of 10 target lesions total
    • -
  • Non-targets can only be assessed as 'present'
    • -
  • Target lesions must have measurements (cannot be assessed as CR, UN/NE, EX)
    • -
-
New Lesion Checks for Follow-ups
-
    -
  • New target lesions must be >= 5 X 5 mm AND >= double the acquisition slice thickness by CT and MR
    • -
  • Up to a max of 5 target lesions per organ
    • -
  • Up to a max of 10 target lesions total
    • -
- -
+

Select one or more Trial Criteria types:

+ {{ #each trialCriteriaTypes}} + + {{ /each }} +
+

Selected Trial Criteria:

+ {{ #each trialCriteriaTypes}} + {{ #if selected }} +
+ {{> Template.dynamic template=descriptionTemplate }} +
+ {{ /if }} + {{ /each }}
diff --git a/Packages/lesiontracker/client/components/optionsModal/optionsModal.js b/Packages/lesiontracker/client/components/optionsModal/optionsModal.js index 0cc2bf0b8..69df7d5d0 100644 --- a/Packages/lesiontracker/client/components/optionsModal/optionsModal.js +++ b/Packages/lesiontracker/client/components/optionsModal/optionsModal.js @@ -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 diff --git a/Packages/lesiontracker/client/components/recistDescription/recistDescription.html b/Packages/lesiontracker/client/components/recistDescription/recistDescription.html new file mode 100644 index 000000000..425ad597b --- /dev/null +++ b/Packages/lesiontracker/client/components/recistDescription/recistDescription.html @@ -0,0 +1,14 @@ + \ No newline at end of file diff --git a/Packages/lesiontracker/lib/TrialCriteriaConstraints.js b/Packages/lesiontracker/lib/TrialCriteriaConstraints.js index 7cbefa342..b8195419e 100644 --- a/Packages/lesiontracker/lib/TrialCriteriaConstraints.js +++ b/Packages/lesiontracker/lib/TrialCriteriaConstraints.js @@ -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]; }; diff --git a/Packages/lesiontracker/lib/TrialResponseCriteria.js b/Packages/lesiontracker/lib/TrialResponseCriteria.js index d8bab5dbd..bf2724443 100644 --- a/Packages/lesiontracker/lib/TrialResponseCriteria.js +++ b/Packages/lesiontracker/lib/TrialResponseCriteria.js @@ -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); diff --git a/Packages/lesiontracker/package.js b/Packages/lesiontracker/package.js index 20ea969cc..3b4112fcc 100644 --- a/Packages/lesiontracker/package.js +++ b/Packages/lesiontracker/package.js @@ -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' ]);