Updates for Timepoint assocation (LT-60) and Conformance Checks (LT-92, LT-93, LT-94)

.gitignore

@@ -3,3 +3,5 @@ docs/
 .meteor/local
 .meteor/meteorite
 node_modules
+Packages/active-entry/helloworld/
+LesionTracker/tests/nightwatch/reports/

.jscsrc

@@ -7,6 +7,7 @@
     "disallowSpacesInFunctionExpression": {
         "beforeOpeningRoundBrace": true
     },
+    "disallowSpacesInsideParentheses": true,
     "disallowKeywordsOnNewLine": ["else"],
     "disallowNewlineBeforeBlockStatements": true,
     "requirePaddingNewLinesAfterUseStrict": true,
@@ -17,9 +18,12 @@
     "requireObjectKeysOnNewLine": true,
     "requireSemicolons": true,
     "requireSpaceAfterBinaryOperators": true,
+    "requireSpaceAfterComma": true,
+    "requireSpacesInFunctionExpression": {
+        "beforeOpeningCurlyBrace": true
+    },
     "requireSpaceBeforeObjectValues": true,
     "requireSpacesInsideObjectBrackets": "all",
-    "requireSpacesInsideArrayBrackets": "all",
     "requireLineBreakAfterVariableAssignment": true,
     "requireSpaceBeforeBinaryOperators": ["+", "-", "/", "*", "=", "==", "===", "!=", "!=="],
     "disallowSpaceAfterPrefixUnaryOperators": ["++", "--", "+", "-"],

LesionTracker/.meteor/packages

@@ -48,3 +48,4 @@ clinical:hipaa-audit-log
 clinical:hipaa-logger
 anti:gagarin@=0.4.11
 check
+aldeed:template-extension@4.0.0

LesionTracker/.meteor/versions

@@ -1,5 +1,6 @@
 accounts-base@1.2.2
 accounts-password@1.1.4
+aldeed:template-extension@4.0.0
 anti:gagarin@0.4.11
 anti:i18n@0.4.3
 arsnebula:reactive-promise@0.9.1
@@ -38,6 +39,7 @@ ddp-server@1.2.2
 deps@1.0.9
 dicomweb@0.0.1
 diff-sequence@1.0.1
+dimseservice@0.0.1
 ecmascript@0.1.6
 ecmascript-runtime@0.2.6
 ejson@1.0.7
@@ -90,6 +92,7 @@ reactive-var@1.0.6
 reload@1.1.4
 retry@1.0.4
 routepolicy@1.0.6
+rwatts:uuid@0.0.2
 service-configuration@1.0.5
 session@1.1.1
 sha@1.0.4

LesionTracker/client/body.styl

@@ -1,30 +1,62 @@
+// TODO: Move all of this into the LesionTracker package
 body
   background-color: #202020
 
-.tab-content {
+.tab-content 
-  height: calc(100% - 40px);
+  height: calc(100% - 40px)
-}
 
-table#tblStudyList thead > tr {
+table#tblStudyList thead > tr 
- background-color: #424242;
+  background-color: #424242
-  color: white;
+  color: white
-}
+
-table#tblStudyList tbody > tr:nth-child(even) {
+table#tblStudyList tbody > tr:nth-child(even) 
-   background-color: #888;
+  background-color: #888
-   color: black;
+  color: black
- }
+ 
-table#tblStudyList tbody > tr:nth-child(odd) {
+table#tblStudyList tbody > tr:nth-child(odd) 
-  background-color: #BBB;
+  background-color: #BBB
-  color: black;
+  color: black
-}
+
-table#tblStudyList tbody > tr:hover{
+table#tblStudyList tbody > tr:hover
   background-color: #009BD2
   color: white
-}
 
-table#tblStudyList tbody > tr > td{
+table#tblStudyList tbody > tr > td
   word-wrap: break-word
-}
 
+/* Mobile devices */
+@media only screen and (min-device-width : 375px) and (max-device-width : 768px)
+  .logoContainer
+    width: 15%
 
+  .navbar-brand
+    img
+      height: 20px
+      margin-top: 10px
+      margin-bottom: 10px
+      margin-right: 5px
 
+    h4.name
+      padding: 1px
+      font-size: 0.3em
+      width: 50%
+
+  table#tblStudyList
+    table-layout: fixed
+    font-size: 0.7em
+
+  #tablist
+    width: 85%
+    overflow-x: auto
+
+  #toolbar .btn-group button
+    width: 40px
+    height: 40px
+
+  .studyDateList
+    margin-top: 5px
+
+@media (max-device-width: 667px)
+  #toolbar .btn-group button
+    width: 35px
+    height: 35px

LesionTracker/client/components/viewer.html

@@ -5,6 +5,7 @@
         {{>nonTargetLesionDialog}}
         {{>nonTargetResponseDialog}}
         {{>timepointTextDialog}}
+        {{ >conformanceCheckFeedback }}
 
         {{>hidingPanel}}
         <div id="viewportAndLesionTable">

LesionTracker/client/components/viewer.js

@@ -3,10 +3,8 @@ Template.viewer.onCreated(function() {
     $(window).on('resize', handleResize);
 
     var self = this;
-
     var firstMeasurementsActivated = false;
-
+    var contentId = this.data.contentId;
-    log.info('viewer onCreated');
 
     OHIF = OHIF || {
             viewer: {}
@@ -16,7 +14,6 @@ Template.viewer.onCreated(function() {
     OHIF.viewer.defaultTool = 'wwwc';
     OHIF.viewer.refLinesEnabled = true;
     OHIF.viewer.isPlaying = {};
-    var contentId = this.data.contentId;
 
     OHIF.viewer.functionList = {
         invert: function(element) {
@@ -42,15 +39,17 @@ Template.viewer.onCreated(function() {
         toggleLesionTrackerTools: toggleLesionTrackerTools,
         clearTools: clearTools,
         lesion: function() {
+            // Used for hotkeys
             toolManager.setActiveTool('lesion');
         },
         nonTarget: function() {
+            // Used for hotkeys
             toolManager.setActiveTool('nonTarget');
         }
-
     };
 
     // The hotkey can also be an array (e.g. ["NUMPAD0", "0"])
+    OHIF.viewer.defaultHotkeys = OHIF.viewer.defaultHotkeys || {};
     OHIF.viewer.defaultHotkeys.toggleLesionTrackerTools = 'O';
     OHIF.viewer.defaultHotkeys.lesion = 'T'; // Target
     OHIF.viewer.defaultHotkeys.nonTarget = 'N'; // Non-target
@@ -65,6 +64,10 @@ Template.viewer.onCreated(function() {
         };
     }
 
+    OHIF.viewer.updateImageSynchronizer = new cornerstoneTools.Synchronizer('CornerstoneNewImage', cornerstoneTools.updateImageSynchronizer);
+
+    log.info('viewer onCreated');
+
     if (ViewerData[contentId].loadedSeriesData) {
         log.info('Reloading previous loadedSeriesData');
         OHIF.viewer.loadedSeriesData = ViewerData[contentId].loadedSeriesData;
@@ -76,8 +79,15 @@ Template.viewer.onCreated(function() {
         ViewerData[contentId].loadedSeriesData = OHIF.viewer.loadedSeriesData;
 
         // Update the viewer data object
+        if (!this.data.timepointIds || this.data.timepointIds.length <= 1) {
+            // Update the viewer data object
+            ViewerData[contentId].viewportColumns = 1;
+            ViewerData[contentId].viewportRows = 1;
+        } else if (this.data.timepointIds.length > 1) {
             ViewerData[contentId].viewportColumns = 2;
             ViewerData[contentId].viewportRows = 1;
+        }
+
         ViewerData[contentId].activeViewport = 0;
         Session.set('ViewerData', ViewerData);
     }
@@ -96,43 +106,29 @@ Template.viewer.onCreated(function() {
 
     self.autorun(function() {
         var patientId = Session.get('patientId');
-        self.subscribe('timepoints', patientId);
+        self.subscribe('singlePatientTimepoints', patientId);
-        self.subscribe('measurements', patientId);
+        self.subscribe('singlePatientMeasurements', patientId);
 
         if (self.subscriptionsReady()) {
             ViewerStudies.find().observe({
                 added: function(study) {
-                    // TODO = Replace this whole section when we have a
+                    // Find the relevant timepoint given the newly added study
-                    // timepoint-to-study association modal
-
-                    // First, check if we have a timepoint related to this
-                    // study date already
                     var timepoint = Timepoints.findOne({
-                        timepointName: study.studyDate
+                        studyInstanceUids: {
+                            $in: [study.studyInstanceUid]
+                        }
                     });
 
-                    // If we do, stop here
+                    if (!timepoint) {
-                    if (timepoint) {
+                        log.warn('Study added to Viewer has not been associated!');
-                        log.warn('A timepoint with that study date already exists!');
                         return;
                     }
                     
-                    // Next, check the first timepoint in the collection
+                    // Update the added document with its related timepointId
-                    var testTimepoint = Timepoints.findOne({});
+                    ViewerStudies.update(study._id, {
-
+                        $set: {
-                    // If it relates to another subject, we need to stop here as well
+                            timepointId: timepoint.timepointId
-                    // because the tab may be changing.
-                    if (testTimepoint && testTimepoint.patientId !== study.patientId) {
-                        log.warn('Timepoints collection related to the wrong subject');
-                        return;
                         }
-
-                    // Otherwise, we need to add a timepoint related to this study date
-                    log.info('Inserting a new timepoint');
-                    Timepoints.insert({
-                        patientId: study.patientId,
-                        timepointName: study.studyDate,
-                        timepointID: uuid.v4()
                     });
                 }
             });
@@ -159,12 +155,17 @@ Template.viewer.onCreated(function() {
                     log.info('Measurement added');
                     syncMeasurementAndToolData(data);
                     updateRelatedElements(data.imageId);
+
+                    TrialResponseCriteria.validateAll();
+                },
+                changed: function(data) {
+                    TrialResponseCriteria.validateAllDelayed();
                 },
                 removed: function(data) {
                     log.info('Measurement removed');
 
                     // Check that this Measurement actually contains timepoint data
-                    if (!data.timepoints) {
+                    if (!data || !data.timepoints) {
                         return;
                     }
 
@@ -175,9 +176,9 @@ Template.viewer.onCreated(function() {
 
                     // Remove the measurement from all the imageIds on which it exists
                     // as toolData
-                    Object.keys(data.timepoints).forEach(function(timepointID) {
+                    Object.keys(data.timepoints).forEach(function(timepointId) {
                         // Clear the toolData for this timepoint
-                        var imageId = data.timepoints[timepointID].imageId;
+                        var imageId = data.timepoints[timepointId].imageId;
                         removeToolDataWithMeasurementId(imageId, toolType, measurementId);
                     });
 
@@ -202,146 +203,29 @@ Template.viewer.onCreated(function() {
                     viewports.each(function(index, element) {
                         cornerstone.updateImage(element);
                     });
-                }
+
-            });
+                    ValidationErrors.remove({
-        }
+                        measurementId: data._id
                     });
 
-    OHIF.viewer.updateImageSynchronizer = new cornerstoneTools.Synchronizer('CornerstoneNewImage', cornerstoneTools.updateImageSynchronizer);
+                    TrialResponseCriteria.validateAll();
+                }
+            });
+        }
+    });
 });
 
-function updateRelatedElements(imageId) {
-    // Get all on-screen elements with this imageId
-    var enabledElements = cornerstone.getEnabledElementsByImageId(imageId);
-
-    // TODO=Check original event to prevent duplicate updateImage calls
-
-    // Loop through these elements
-    enabledElements.forEach(function(enabledElement) {
-        // Update the display so the tool is removed
-        var element = enabledElement.element;
-        cornerstone.updateImage(element);
-    });
-}
-
-function syncMeasurementAndToolData(data) {
-    // Check what toolType we should be adding this to, based on the isTarget value
-    // of the stored Measurement
-    var toolType = data.isTarget ? 'lesion' : 'nonTarget';
-    var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
-
-    // Loop through the timepoint data for this measurement
-    Object.keys(data.timepoints).forEach(function(key) {
-        var storedData = data.timepoints[key];
-        var imageId = storedData.imageId;
-
-        if (!toolState[imageId]) {
-            toolState[imageId] = {};
-        }
-
-        // This is probably not the best approach to prevent duplicates
-        if (toolState[imageId][toolType] && toolState[imageId][toolType].data) {
-            var measurementHasNoIdYet = false;
-            toolState[imageId][toolType].data.forEach(function(measurement) {
-                if (measurement.id === 'notready') {
-                    measurementHasNoIdYet = true;
-                    return false;
-                }
-            });
-
-            // Stop here if it appears that we are creating this measurement right now,
-            // and would not like this function to add another copy of it to the toolData
-            if (measurementHasNoIdYet === true) {
-                return;
-            }
-        }
-
-        if (!toolState[imageId][toolType]) {
-            toolState[imageId][toolType] = {
-                data: []
-            };
-        } else {
-            var alreadyExists = false;
-            if (toolState[imageId][toolType].data.length) {
-                toolState[imageId][toolType].data.forEach(function(measurement) {
-                    if (measurement.id === data._id) {
-                        alreadyExists = true;
-
-                        // Update the toolData lesionNumber from the Measurement
-                        measurement.lesionNumber = data.lesionNumber;
-                        return false;
-                    }
-                });
-            }
-
-            if (alreadyExists === true) {
-                return;
-            }
-        }
-
-        // Create measurementData structure based on the lesion data at this timepoint
-        // We will add this into the toolData for this imageId
-        var measurementData = storedData;
-        measurementData.isTarget = data.isTarget;
-        measurementData.lesionNumber = data.lesionNumber;
-        measurementData.measurementText = data.measurementText;
-        measurementData.isDeleted = data.isDeleted;
-        measurementData.location = data.location;
-        measurementData.locationUID = data.locationUID;
-        measurementData.patientId = patientId;
-        measurementData.visible = data.visible;
-        measurementData.active = data.active;
-        measurementData.uid = data.uid;
-        measurementData.id = data._id;
-
-        toolState[imageId][toolType].data.push(measurementData);
-    });
-}
-
 Template.viewer.onRendered(function() {
     // Enable hotkeys
     enableHotkeys();
 
-    // Set lesion tool buttons as disable if pixel spacing is not available for active element
+    // Set lesion tool buttons as disabled if pixel spacing is not available for active element
-    this.autorun(function(){
+    this.autorun(pixelSpacingAutorunCheck);
-        if (!Session.get('ViewerData') || Session.get('activeViewport') === undefined) {
-            return;
-        }
-
-        var activeViewportIndex = Session.get('activeViewport');
-        var viewports = $(".imageViewerViewport");
-        var element =  viewports.get(activeViewportIndex);
-
-        // Check element has .empty class
-        if (element.classList.contains('empty')) {
-            setLesionToolButtonsDisable(true);
-            return;
-        }
-
-        try {
-            var enabledElement = cornerstone.getEnabledElement(element);
-            if (!enabledElement || !enabledElement.image ||
-                !enabledElement.image.rowPixelSpacing ||
-                !enabledElement.image.columnPixelSpacing) {
-                // Disable Lesion Tools and Buttons
-                toolManager.setActiveTool("wwwc", viewports);
-                cornerstoneTools.lesion.disable(element);
-                cornerstoneTools.nonTarget.disable(element);
-                setLesionToolButtonsDisable(true);
-            } else{
-                // Enable Lesion Buttons
-                setLesionToolButtonsDisable(false);
-            }
-        } catch(error) {
-            return;
-        }
-    });
-
 });
 
 Template.viewer.onDestroyed(function() {
     log.info('onDestroyed');
-    console.log("viewer destroyed!");
+    console.log('viewer destroyed!');
 
     // Remove the Window resize listener
     $(window).off('resize', handleResize);
@@ -350,6 +234,9 @@ Template.viewer.onDestroyed(function() {
 });
 
 Template.viewer.events({
+    'CornerstoneToolsMeasurementAdded .imageViewerViewport': function(e, template, eventData) {
+        handleMeasurementAdded(e, eventData);
+    },
     'CornerstoneToolsMeasurementModified .imageViewerViewport': function(e, template, eventData) {
         handleMeasurementModified(e, eventData);
     },
@@ -357,43 +244,3 @@ Template.viewer.events({
         handleMeasurementRemoved(e, eventData);
     }
 });
-
-function handleMeasurementModified(e, eventData) {
-    log.info('CornerstoneToolsMeasurementModified');
-    var measurementData = eventData.measurementData;
-
-    switch (eventData.toolType) {
-        case 'nonTarget':
-        case 'lesion':
-            LesionManager.updateLesionData(measurementData);
-            break;
-    }
-}
-
-function handleMeasurementRemoved(e, eventData) {
-    log.info('CornerstoneToolsMeasurementRemoved');
-    var measurementData = eventData.measurementData;
-
-    switch (eventData.toolType) {
-        case 'nonTarget':
-        case 'lesion':
-            var measurement = Measurements.findOne(measurementData.id, {
-                reactive: false
-            });
-
-            if (!measurement) {
-                return;
-            }
-
-            clearMeasurementTimepointData(measurement._id, measurementData.timepointID);
-            break;
-    }
-}
-
-// Set enablement of Lesion Tools Buttons
-function setLesionToolButtonsDisable (status) {
-    var buttons = [$("button#lesion"), $("button#nonTarget")];
-    buttons.forEach(function(btn){
-        btn.prop("disabled", status);
-    });
-}

LesionTracker/client/mobileStyles.css

@@ -1,51 +0,0 @@
-
-/* Mobile devices */
-
-@media only screen and (min-device-width : 375px) and (max-device-width : 768px){
-
-    .logoContainer {
-        width: 15%;
-    }
-
-    .navbar-brand img {
-        height: 20px;
-        margin-top: 10px;
-        margin-bottom: 10px;
-        margin-right: 5px;
-    }
-
-    .navbar-brand h4.name {
-        padding: 1px;
-        font-size: 0.3em;
-        width: 50%;;
-    }
-
-    table#tblStudyList {
-        table-layout: fixed;
-        font-size: 0.7em;
-    }
-
-    #tablist {
-        width: 85%;
-        overflow-x: auto;
-    }
-
-    #toolbar .btn-group button {
-        width: 40px;
-        height: 40px;
-    }
-
-    .studyDateList {
-        margin-top: 5px;
-    }
-}
-
-
-@media (max-device-width: 667px) {
-
-    #toolbar .btn-group button {
-        width: 35px;
-        height: 35px;
-    }
-}
-

LesionTracker/client/routeHooks.js

@@ -1,5 +0,0 @@
-Router.onBeforeAction(function() {
-
-    // User is logged in, go ahead and route them
-    this.next();
-});

LesionTracker/client/routes.js

@@ -11,15 +11,17 @@ Object.keys(ViewerData).forEach(function(contentId) {
 });
 
 Router.configure({
-    layoutTemplate: 'layoutLesionTracker',
+    layoutTemplate: 'lesionTrackerLayout',
-    loadingTemplate: 'layoutLesionTracker'
+    loadingTemplate: 'lesionTrackerLayout',
+    notFoundTemplate: 'notFound'
 });
 
 Router.onBeforeAction('loading');
 
 var data = {
     additionalTemplates: [
-        'associationModal'
+        'associationModal',
+        'optionsModal'
     ]
 };
 
@@ -35,24 +37,22 @@ Router.route('/worklist', function() {
     this.render('worklist', routerOptions);
 });
 
-Router.route('/viewer/:_id', {
+Router.route('/viewer/timepoints/:_id', {
-    layoutTemplate: 'layoutLesionTracker',
+    layoutTemplate: 'lesionTrackerLayout',
     name: 'viewer',
     onBeforeAction: function() {
-        log.info('Router GetStudyMetadata');
+        var timepointId = this.params._id;
-
-        var studyInstanceUid = this.params._id;
 
         // Check if this study is already loaded in a tab
         // If it is, stop here so we don't keep adding tabs on hot-code reloads
-        var tab = WorklistTabs.find({
+        var tab = WorklistTabs.findOne({
-            studyInstanceUid: studyInstanceUid
+            timepointId: timepointId
-        }).fetch();
+        });
         if (tab) {
             return;
         }
 
         this.render('worklist', routerOptions);
-        openNewTab(studyInstanceUid);
+        openNewTabWithTimepoint(timepointId);
     }
 });

LesionTracker/client/stylesheets/docking-container.css

@@ -1,55 +0,0 @@
-/*****************************/
-/* Toggle */
-/*****************************/
-.dockingContainer, .collapseVertical, .collapseHorizontal {
-    -o-transition: all 0.3s ease-out;
-    -ms-transition: all 0.3s ease-out;
-    -moz-transition: all 0.3s ease-out;
-    -webkit-transition: all 0.3s ease-out;
-    transition: all 0.3s ease-out;
-}
-
-.dockingContainer {
-    -o-transition: all 0.3s ease-out;
-    -ms-transition: all 0.3s ease-out;
-    -moz-transition: all 0.3s ease-out;
-    -webkit-transition: all 0.3s ease-out;
-    transition: all 0.3s ease-out;
-}
-
-.collapseVertical {
-    opacity: 0;
-    height: 0;
-    border: none;
-}
-
-.collapseHorizontal {
-    width: 30px;
-}
-
-.btnCollapse{
-    position: absolute;
-    top: 0;
-    left: 0;
-    display: block;
-    width: 25px;
-    height: 25px;
-    line-height: 25px;
-    padding: 0;
-    border: 0;
-    border-top: 1px solid #e6e6e6;
-    background: #f6f6f6;
-    color: #666;
-    font-size: 0.875rem;
-    text-align: center;
-    cursor: pointer;
-    z-index: 100;
-}
-
-.btnCollapseIcon-collapse{
-    -moz-transform: rotate(180deg);
-    -ms-transform: rotate(180deg);
-    -o-transform: rotate(180deg);
-    -webkit-transform: rotate(180deg);
-    transform: rotate(180deg);
-}

LesionTracker/defaultSettings.js

@@ -1,15 +1,7 @@
 Meteor.startup(function() {
-    if (Meteor.settings.dicomWeb) {
-        console.log('dicomWeb settings defined!');
-        console.log(Meteor.settings);
-        return;
-    }
-
-    console.log('Using default LesionTracker dicomWeb settings');
     Meteor.settings = {
         dicomWeb: {
-            endpoints: [
+            endpoints: [{
-          {
                 name: 'Orthanc',
                 wadoUriRootNOTE: 'either this uri is not correct for wado-uri or wado-uri is not configured on orthanc currently',
                 wadoUriRoot: 'http://localhost:8043/wado',
@@ -23,8 +15,16 @@ Meteor.startup(function() {
                   logResponses: false,
                   logTiming: true
               }
-          }
+            }]
-        ]
+        },
-        }
+        dimse: {
+            host: 'localhost',
+            port: 4242,
+            hostAE: 'ORTHANC'
+        },
+        defaultServiceType: 'dicomWeb'
+        //defaultServiceType: 'dimse'
     };
+
+    console.log('Using default LesionTracker settings with service: ' + Meteor.settings.defaultServiceType);
 });

OHIFViewer/.meteor/versions

@@ -77,6 +77,7 @@ reactive-var@1.0.6
 reload@1.1.4
 retry@1.0.4
 routepolicy@1.0.6
+rwatts:uuid@0.0.2
 service-configuration@1.0.5
 session@1.1.1
 sha@1.0.4

Packages/cornerstone/client/cornerstoneWADORSImageLoader.js

@@ -1,77 +0,0 @@
-cornerstoneWADORSImageLoader = {
-  internal : {
-    nextIndex: 0,
-    imageIds : []
-  }
-};
-
-cornerstoneWADORSImageLoader.addImage = function(image) {
-  var index = cornerstoneWADORSImageLoader.internal.nextIndex++;
-  cornerstoneWADORSImageLoader.internal.imageIds[index] = image;
-  var imageId = 'wadors:' + index;
-  return imageId;
-};
-
-function getMinMax(storedPixelData)
-{
-  // we always calculate the min max values since they are not always
-  // present in DICOM and we don't want to trust them anyway as cornerstone
-  // depends on us providing reliable values for these
-  var min = 65535;
-  var max = -32768;
-  var numPixels = storedPixelData.length;
-  var pixelData = storedPixelData;
-  for(var index = 0; index < numPixels; index++) {
-    var spv = pixelData[index];
-    // TODO: test to see if it is faster to use conditional here rather than calling min/max functions
-    min = Math.min(min, spv);
-    max = Math.max(max, spv);
-  }
-
-  return {
-    min: min,
-    max: max
-  };
-}
-
-cornerstone.registerImageLoader('wadors', function(imageId) {
-  var index = imageId.substring(7);
-  var image = cornerstoneWADORSImageLoader.internal.imageIds[index];
-
-  var deferred = $.Deferred();
-
-  var mediaType;// = 'image/dicom+jp2';
-
-  DICOMWeb.getImageFrame(image.uri, mediaType).then(function(result) {
-    //console.log(result);
-    // TODO: add support for retrieving compressed pixel data
-    var storedPixelData;
-    if(image.instance.bitsAllocated === 16) {
-      if(image.instance.pixelRepresentation === 0) {
-        storedPixelData = new Uint16Array(result.arrayBuffer, result.offset, result.length / 2);
-      } else {
-        storedPixelData = new Int16Array(result.arrayBuffer, result.offset, result.length / 2);
-      }
-    } else if(image.instance.bitsAllocated === 8) {
-      storedPixelData = new Uint8Array(result.arrayBuffer, result.offset, result.length);
-    }
-
-    // TODO: handle various color space conversions
-
-    var minMax = getMinMax(storedPixelData);
-    image.imageId = imageId;
-    image.minPixelValue = minMax.min;
-    image.maxPixelValue = minMax.max;
-    image.render = cornerstone.renderGrayscaleImage;
-    image.getPixelData = function() {
-      return storedPixelData;
-    };
-    //console.log(image);
-    deferred.resolve(image);
-  }).catch(function(reason) {
-    deferred.reject(reason);
-  });
-
-  return deferred;
-});
-

Packages/cornerstone/client/dicomParser.js

@@ -1,4 +1,4 @@
-/*! dicom-parser - v1.2.0 - 2015-11-02 | (c) 2014 Chris Hafey | https://github.com/chafey/dicomParser */
+/*! dicom-parser - v1.2.1 - 2016-02-07 | (c) 2014 Chris Hafey | https://github.com/chafey/dicomParser */
 (function (root, factory) {
 
     // node.js
@@ -66,6 +66,7 @@ var dicomParser = (function(dicomParser) {
         function getDataSetByteStream(transferSyntax, position) {
             if(transferSyntax === '1.2.840.10008.1.2.1.99')
             {
+              // https://github.com/nodeca/pako
               if(typeof(pako) === "undefined") {
                 throw 'dicomParser.parseDicom: deflated transfer syntax encountered but pako not loaded';
               }
@@ -936,8 +937,9 @@ var dicomParser = (function (dicomParser)
         {
             throw "dicomParser.ByteStream: missing required parameter 'byteArray'";
         }
-        if((byteArray instanceof Uint8Array) === false) {
+        if((byteArray instanceof Uint8Array) === false &&
-            throw 'dicomParser.ByteStream: parameter byteArray is not of type Uint8Array';
+          (byteArray instanceof Buffer) === false ) {
+            throw 'dicomParser.ByteStream: parameter byteArray is not of type Uint8Array or Buffer';
         }
         if(position < 0)
         {
@@ -2253,7 +2255,7 @@ var dicomParser = (function (dicomParser)
     dicomParser = {};
   }
 
-  dicomParser.version = "1.2.0";
+  dicomParser.version = "1.2.1";
 
   return dicomParser;
 }(dicomParser));

Packages/cornerstone/package.js

@@ -1,30 +1,45 @@
 Package.describe({
-  name: "cornerstone",
+    name: 'cornerstone',
-  summary: "Cornerstone Web-based Medical Imaging libraries",
+    summary: 'Cornerstone Web-based Medical Imaging libraries',
     version: '0.0.1'
 });
 
-Package.onUse(function (api) {
+Package.onUse(function(api) {
     api.versionsFrom('1.2.0.2');
 
     api.use('jquery');
+    api.use('dicomweb');
 
-    api.addFiles('client/cornerstone.js', 'client', {bare: true});
+    api.addFiles('client/cornerstone.js', 'client', {
-    api.addFiles('client/cornerstoneMath.js', 'client', {bare: true});
+        bare: true
-    api.addFiles('client/cornerstoneTools.js', 'client', {bare: true});
+    });
-    api.addFiles('client/cornerstoneWADOImageLoader.js', 'client', {bare: true});
+    api.addFiles('client/cornerstoneMath.js', 'client', {
-    api.addFiles('client/cornerstoneWADORSImageLoader.js', 'client', {bare: true});
+        bare: true
-    api.addFiles('client/dicomParser.js', 'client', {bare: true});
+    });
-    api.addFiles('client/hammer.js', 'client', {bare: true});
+    api.addFiles('client/cornerstoneTools.js', 'client', {
+        bare: true
+    });
+    api.addFiles('client/cornerstoneWADOImageLoader.js', 'client', {
+        bare: true
+    });
+    api.addFiles('client/dicomParser.js', 'client', {
+        bare: true
+    });
+    api.addFiles('client/hammer.js', 'client', {
+        bare: true
+    });
 
-    api.addFiles('client/measurementManager.js', 'client', {bare: true});
+    api.addFiles('client/measurementManager.js', 'client', {
-    api.addFiles('client/measurementManagerExample.js', 'client', {bare: true});
+        bare: true
+    });
+    api.addFiles('client/measurementManagerExample.js', 'client', {
+        bare: true
+    });
 
-    api.export("cornerstone", 'client');
+    api.export('cornerstone', 'client');
-    api.export("cornerstoneMath", 'client');
+    api.export('cornerstoneMath', 'client');
-    api.export("cornerstoneTools", 'client');
+    api.export('cornerstoneTools', 'client');
-    api.export("cornerstoneWADOImageLoader", 'client');
+    api.export('cornerstoneWADOImageLoader', 'client');
-    api.export("cornerstoneWADORSImageLoader", 'client');
+    api.export('dicomParser', ['client', 'server']);
-    api.export("dicomParser", ['client', 'server']);
 });
 

Packages/dicomweb/lib/findIndexOfString.js

@@ -1,52 +0,0 @@
-/**
- * Converts a String to a UInt8 array of character codes
- * @param {String} str Input string
- * @returns {Uint8Array} Uint8 Array of character codes
- */
-function stringToUint8Array(str) {
-    var uint = new Uint8Array(str.length);
-    for (var i = 0,j = str.length;i< j;i++){
-        uint[i] = str.charCodeAt(i);
-    }
-
-    return uint;
-}
-
-function checkToken(token, data, dataOffset) {
-    if (dataOffset + token.length > data.length) {
-        //console.log('dataOffset >> ', dataOffset);
-        return false;
-    }
-
-    for (var i = 0; i < token.length; i++) {
-        if (token[i] !== data[endIndex++]) {
-            if (endIndex > 520000) {
-                console.log('token=',uint8ArrayToString(token));
-                console.log('data=', uint8ArrayToString(data, dataOffset, endIndex - dataOffset));
-                console.log('miss at %d %s dataOffset=%d', i, String.fromCharCode(data[endIndex]), endIndex);
-                console.log('miss at %d %s dataOffset=%d', i, String.fromCharCode(token[endIndex]), endIndex);
-            }
-
-            return false;
-        }
-    }
-
-    return true;
-}
-
-findIndexOfString = function(data, str, offset) {
-    offset = offset || 0;
-
-    var token = stringToUint8Array(str);
-
-    for (var i = offset; i < data.length; i++) {
-        if (data[i] === token[0]) {
-            //console.log('match @', i);
-            if (checkToken(token, data, i)) {
-                return i;
-            }
-        }
-    }
-
-    return -1;
-};

Packages/dicomweb/lib/uint8ArrayToString.js

@@ -1,18 +0,0 @@
-/**
- * Converts a Uint8 array to a string
- * @param data
- * @param offset
- * @param length
- * @returns {string}
- */
-uint8ArrayToString = function(data, offset, length) {
-    offset = offset || 0;
-    length = length || data.length - offset;
-    var str = '';
-
-    for (var i = offset; i < offset + length; i++) {
-        str += String.fromCharCode(data[i]);
-    }
-
-    return str;
-};

Packages/dicomweb/package.js

@@ -9,16 +9,11 @@ Package.onUse(function(api) {
 
     // DICOMWeb API functions
     api.addFiles('server/namespace.js', 'server');
-    api.addFiles('server/getImageFrame.js', 'server');
     api.addFiles('server/getJSON.js', 'server');
     api.addFiles('server/getName.js', 'server');
     api.addFiles('server/getNumber.js', 'server');
     api.addFiles('server/getString.js', 'server');
 
-    // Helper functions
+    api.export('DICOMWeb', ['client', 'server']);
-    api.addFiles('lib/findIndexOfString.js', 'server');
-    api.addFiles('lib/uint8ArrayToString.js', 'server');
-
-    api.export('DICOMWeb', 'server');
 });
 

Packages/dicomweb/server/getImageFrame.js

@@ -1,74 +0,0 @@
-function findBoundary(header) {
-    for (var i = 0; i < header.length; i++) {
-        if (header[i].substr(0,2) === '--') {
-            return header[i];
-        }
-    }
-
-    return undefined;
-}
-
-function findContentType(header) {
-    for (var i = 0; i < header.length; i++) {
-        if (header[i].substr(0,13) === 'Content-Type:') {
-            return header[i].substr(13).trim();
-        }
-    }
-
-    return undefined;
-}
-
-DICOMWeb.getImageFrame = function(uri, mediaType) {
-    mediaType = mediaType || 'application/octet-stream';
-
-    return new Promise(function(resolve, reject) {
-        var xhr = new XMLHttpRequest();
-        xhr.responseType = 'arraybuffer';
-        xhr.open('get', uri, true);
-        xhr.setRequestHeader('Accept', 'multipart/related;type=' + mediaType);
-        xhr.onreadystatechange = function(oEvent) {
-            // TODO: consider sending out progress messages here as we receive the pixel data
-            if (xhr.readyState === 4) {
-                if (xhr.status === 200) {
-                    // request succeeded, Parse the multi-part mime response
-                    var imageFrameAsArrayBuffer = xhr.response;
-                    var response = new Uint8Array(xhr.response);
-                    // First look for the multipart mime header
-                    var tokenIndex = findIndexOfString(response, '\n\r\n');
-                    if (tokenIndex === -1) {
-                        reject('invalid response - no multipart mime header');
-                    }
-
-                    var header = uint8ArrayToString(response, 0, tokenIndex);
-                    // Now find the boundary  marker
-                    var split = header.split('\r\n');
-                    var boundary = findBoundary(split);
-                    if (!boundary) {
-                        reject('invalid response - no boundary marker');
-                    }
-
-                    var offset = tokenIndex + 4; // skip over the \n\r\n
-
-                    // find the terminal boundary marker
-                    var endIndex = findIndexOfString(response, boundary, offset);
-                    if (endIndex === -1) {
-                        reject('invalid response - terminating boundary not found');
-                    }
-                    // return the info for this pixel data
-                    var length = endIndex - offset - 1;
-                    resolve({
-                        contentType: findContentType(split),
-                        arrayBuffer: imageFrameAsArrayBuffer,
-                        offset: offset,
-                        length: length
-                    });
-                } else {
-                    // request failed, reject the deferred
-                    reject(xhr.response);
-                }
-            }
-        };
-
-        xhr.send();
-    });
-};

Packages/dicomweb/server/getJSON.js

@@ -2,7 +2,7 @@ DICOMWeb.getJSON = function(url, options) {
     var getOptions = {
         headers: {
             Accept: 'application/json'
-    },
+        }
     };
 
     if (options.auth) {

Packages/dimse-service/etc/sampleOrthancConfig.json

@@ -1,6 +0,0 @@
-// The list of the known DICOM modalities
-// If you are running Orthanc with Docker, you need to put the contents of this file in 
-// /etc/orthanc/orthanc.json
-"DicomModalities" : {
-    "OHIFDCM" : [ "OHIFDCM", "localhost", 3000 ]
-},

Packages/dimseservice/etc/sampleOrthancConfig.json

@@ -0,0 +1,5 @@
+// The list of the known DICOM modalities
+// If you are running Orthanc , you need to put the contents of this file in its Configuration file
+"DicomModalities" : {
+    "OHIFDCM" : [ "OHIFDCM", "localhost", 3000 ]
+},

Packages/dimseservice/server/DIMSE.js

@@ -8,11 +8,16 @@ DIMSE.associate = function(contexts, callback) {
         port = Meteor.settings.dimse.port,
         ae = Meteor.settings.dimse.hostAE;
 
+    console.log("Associating via DIMSE");
+    console.log(Meteor.settings.dimse);
+
     var client = net.connect({
         host: host,
         port: port
-        },
+    });
-        function() { //'connect' listener
+
+    client.on('connect', function() {
+        //'connect' listener
         console.log('==Connected');
 
         var conn = new Connection(client, {
@@ -20,15 +25,21 @@ DIMSE.associate = function(contexts, callback) {
                 split: false
             }
         });
+
         conn.associate({
             contexts: contexts,
             hostAE: ae
         }, function(pdu) {
             // associated
             console.log('==Associated');
+
             callback.call(conn, pdu);
         });
     });
+
+    client.on('error', function(error) {
+        throw error;
+    });
 };
 
 DIMSE.retrievePatients = function(params) {

Packages/lesiontracker/both/collections.js

@@ -1,2 +1,5 @@
 Timepoints = new Meteor.Collection('timepoints');
+Studies = new Meteor.Collection('studies');
 Measurements = new Meteor.Collection('measurements');
+
+WorklistSubscriptions = ['studies', 'timepoints'];

Packages/lesiontracker/client/collections/LesionLocations.js

@@ -6,7 +6,8 @@ LesionLocations.insert({
     location: 'Liver Left',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -15,7 +16,8 @@ LesionLocations.insert({
     location: 'Liver Right',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -24,7 +26,8 @@ LesionLocations.insert({
     location: 'Liver Caudate',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -33,7 +36,8 @@ LesionLocations.insert({
     location: 'Lung LLL',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -42,7 +46,8 @@ LesionLocations.insert({
     location: 'Lung LUL',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -51,7 +56,8 @@ LesionLocations.insert({
     location: 'Lung RLL',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -60,7 +66,8 @@ LesionLocations.insert({
     location: 'Lung RML',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -69,7 +76,8 @@ LesionLocations.insert({
     location: 'Lung RUL',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -78,7 +86,8 @@ LesionLocations.insert({
     location: 'Pleura Left',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -87,7 +96,8 @@ LesionLocations.insert({
     location: 'Pleura Right',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -96,7 +106,8 @@ LesionLocations.insert({
     location: 'Kidney Left',
     hasDescription: false,
     description: '',
-    selected: false
+    selected: false,
+    isNodal: false
 });
 
 LesionLocations.insert({
@@ -104,5 +115,7 @@ LesionLocations.insert({
     group: 'kidney',
     location: 'Kidney Right',
     hasDescription: false,
-    description: ''
+    description: '',
+    selected: false,
+    isNodal: false
 });

Packages/lesiontracker/client/collections/PatientLocations.js

@@ -0,0 +1 @@
+PatientLocations = new Meteor.Collection(null);

Packages/lesiontracker/client/compatibility/LesionManager.js

@@ -1,190 +0,0 @@
-var LesionManager = (function() {
-    PatientLocations = new Meteor.Collection(null);
-
-    /**
-     * Retrieve a location name (e.g. Liver Right) from the
-     * PatientLocations Collection by id, if it exists. Otherwise,
-     * return an empty string.
-     *
-     * @param id
-     * @returns {*|string}
-     */
-    function getLocationName(id) {
-        var locationObject = PatientLocations.findOne(id);
-        if (!locationObject || !locationObject.location) {
-            return '';
-        }
-        
-        return locationObject.location;
-    }
-
-    /**
-     * Update the Timepoint object for a specific Measurement.
-     * If no measurement exists yet, one will be created.
-     *
-     * Input is toolData from the lesion or nonTarget tool
-     *
-     * @param lesionData
-     */
-    function updateLesionData(lesionData) {
-        // Find the related Timepoint from the Timepoints Collection
-        var timepointID = lesionData.timepointID;
-        var timepoint = Timepoints.findOne({
-            timepointID: timepointID
-        });
-        if (!timepoint) {
-            log.warn('Timepoint in an image is not present in the Timepoints Collection?');
-            return;
-        }
-
-        // Find the specific lesion to be updated
-        var existingMeasurement;
-        if (lesionData.id && lesionData.id !== 'notready') {
-            existingMeasurement = Measurements.findOne(lesionData.id);
-        } else {
-            existingMeasurement = Measurements.findOne({
-                lesionNumber: lesionData.lesionNumber,
-                isTarget: lesionData.isTarget
-            });
-        }
-
-        // Create a structure for the timepointData based
-        // on this Lesion's toolData
-        var timepointData = {
-            seriesInstanceUid: lesionData.seriesInstanceUid,
-            studyInstanceUid: lesionData.studyInstanceUid,
-            handles: lesionData.handles,
-            imageId: lesionData.imageId
-        };
-
-        if (lesionData.isTarget === true) {
-            timepointData.shortestDiameter = lesionData.widthMeasurement;
-            timepointData.longestDiameter = lesionData.measurementText;
-        } else {
-            timepointData.response = lesionData.response;
-        }
-
-        // If no such lesion exists, we need to add one
-        if (!existingMeasurement) {
-            // Create a data structure for the Measurement
-            // based on the current tool data
-            var measurement = {
-                lesionNumber: lesionData.lesionNumber,
-                isTarget: lesionData.isTarget,
-                patientId: lesionData.patientId,
-                id: lesionData.id
-            };
-
-            // Retrieve the location name given the locationUID
-            if (lesionData.locationUID !== undefined) {
-                measurement.location = getLocationName(lesionData.locationUID);
-            }
-
-            // Add toolData parameters to the Measurement at this Timepoint
-            measurement.timepoints = {};
-            measurement.timepoints[timepointID] = timepointData;
-
-            // Set a flag to prevent duplication of toolData
-            measurement.toolDataInsertedManually = true;
-
-            // Increment and store the absolute Lesion Number for this Measurement
-            measurement.lesionNumberAbsolute = Measurements.find().count() + 1;
-
-            // Insert this into the Measurements Collection
-            // Save the ID into the toolData (not sure if this works?)
-            measurement.id = Measurements.insert(measurement);
-
-            // Update the database entry so it can be readded next time the study is loaded
-            Measurements.update(measurement.id, {
-                $set: {
-                    toolDataInsertedManually: false
-                }
-            });
-        } else {
-            lesionData.id = existingMeasurement._id;
-
-            // Update timepoints from lesion data
-            existingMeasurement.timepoints[timepointID] = timepointData;
-
-            Measurements.update(existingMeasurement._id, {
-                $set: {
-                    timepoints: existingMeasurement.timepoints
-                }
-            });
-        }
-    }
-
-    /**
-     * Returns new lesion number according to timepointID
-     * @param timepointID
-     * @param isTarget
-     * @returns {*}
-     */
-    function getNewLesionNumber(timepointID, isTarget) {
-        // Get all current lesion measurements
-        var numMeasurements = Measurements.find({
-            isTarget: isTarget
-        }).count();
-
-        // If no measurements exist yet, start at 1
-        if (!numMeasurements) {
-            return 1;
-        }
-
-        // Find related measurements (i.e. target or non-target)
-        var measurements = Measurements.find({
-            isTarget: isTarget
-        }, {
-            sort: {
-                lesionNumber: 1
-            }
-        }).fetch();
-
-        // If measurements exist, find the last lesion number
-        // from the given timepoint
-        var lesionNumberCounter = 1;
-
-        // Search through every Measurement to see which ones
-        // already have data for this Timepoint, if we find one that
-        // doesn't have data, we will stop there and use that as the
-        // current Measurement
-        measurements.every(function(measurement) {
-            // If this measurement has no data for this Timepoint,
-            // use this as the current Measurement
-            if (!measurement.timepoints[timepointID]) {
-                lesionNumberCounter = measurement.lesionNumber;
-                return false;
-            }
-
-            lesionNumberCounter++;
-            return true;
-        });
-        return lesionNumberCounter;
-    }
-
-    /**
-     * If the current Lesion Number already exists
-     * for any other timepoint, returns lesion locationUID
-     * @param lesionData
-     * @returns {*}
-     */
-    function lesionNumberExists(lesionData) {
-        var measurement = Measurements.findOne({
-            lesionNumber: lesionData.lesionNumber,
-            isTarget: lesionData.isTarget
-        });
-
-        if (!measurement) {
-            return;
-        }
-
-        return measurement.locationUID;
-    }
-
-    return {
-        updateLesionData: updateLesionData,
-        getNewLesionNumber: getNewLesionNumber,
-        lesionNumberExists: lesionNumberExists,
-        getLocationName: getLocationName
-    };
-})();

Packages/lesiontracker/client/compatibility/lesionTool.js

@@ -50,6 +50,11 @@
         };
         var config = cornerstoneTools.lesion.getConfiguration();
 
+        // Set lesion number and lesion name
+        if (measurementData.lesionNumber === undefined) {
+            config.setLesionNumberCallback(measurementData, mouseEventData, doneCallback);
+        }
+
         // associate this data with this imageId so we can render it and manipulate it
         cornerstoneTools.addToolState(element, toolType, measurementData);
 
@@ -76,11 +81,6 @@
         // Bind a one-time event listener for the Esc key
         $(element).one('keydown', cancelCallback);
 
-        // Set lesion number and lesion name
-        if (measurementData.lesionNumber === undefined) {
-            config.setLesionNumberCallback(measurementData, mouseEventData, doneCallback);
-        }
-
         cornerstone.updateImage(element);
 
         cornerstoneTools.moveNewHandle(mouseEventData, toolType, measurementData, measurementData.handles.end, function() {
@@ -217,8 +217,7 @@
             widthMeasurement: 0,
             perpendicularMeasurement: 0,
             isDeleted: false,
-            isTarget: true,
+            isTarget: true
-            uid: uuid.v4()
         };
         return measurementData;
     }

Packages/lesiontracker/client/compatibility/nonTargetTool.js

@@ -51,6 +51,13 @@
             mouseButtonMask: mouseEventData.which
         };
 
+        var config = cornerstoneTools.nonTarget.getConfiguration();
+
+        // Set lesion number and lesion name
+        if (measurementData.lesionNumber === undefined) {
+            config.setLesionNumberCallback(measurementData, mouseEventData, doneCallback);
+        }
+
         // associate this data with this imageId so we can render it and manipulate it
         cornerstoneTools.addToolState(mouseEventData.element, toolType, measurementData);
 
@@ -77,13 +84,6 @@
         // Bind a one-time event listener for the Esc key
         $(element).one('keydown', cancelCallback);
 
-        var config = cornerstoneTools.nonTarget.getConfiguration();
-
-        // Set lesion number and lesion name
-        if (measurementData.lesionNumber === undefined) {
-            config.setLesionNumberCallback(measurementData, mouseEventData, doneCallback);
-        }
-
         cornerstone.updateImage(element);
 
         cornerstoneTools.moveNewHandle(mouseEventData, toolType, measurementData, measurementData.handles.end, function() {
@@ -101,6 +101,8 @@
             $(element).on('CornerstoneToolsMouseDown', eventData, cornerstoneTools.nonTarget.mouseDownCallback);
             $(element).on('CornerstoneToolsMouseDownActivate', eventData, cornerstoneTools.nonTarget.mouseDownActivateCallback);
 
+            $(element).off('keydown', cancelCallback);
+
             cornerstone.updateImage(mouseEventData.element);
         });
     }

Packages/lesiontracker/client/compatibility/scaleOverlayTool.js

@@ -50,11 +50,10 @@
                 x: config.horizontalLine.start.x + i * config.horizontalMinorTick,
                 y: 0
             };
-            if (i% 5 === 0) {
 
+            if (i% 5 === 0) {
                 endPoint.y = config.horizontalLine.start.y - config.majorTickLength;
             } else {
-
                 endPoint.y = config.horizontalLine.start.y - config.minorTickLength;
             }
 

Packages/lesiontracker/client/components/associationModal/associationModal.html

@@ -10,8 +10,8 @@
                     {{ >studyAssociationTable }}
                 </div>
                 <div class="modal-footer">
-                    <button type="button" class="btn btn-primary" id="saveAssociations" data-dismiss="modal" data-toggle="modal" data-target="#associationModal">Save</button>
+                    <button type="button" class="btn btn-primary" id="saveAssociations">Save</button>
-                    <button type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
+                    <button type="button" class="btn btn-secondary" data-dismiss="modal" id='cancelAssociation'>Cancel</button>
                 </div>
             </div>
         </div>

Packages/lesiontracker/client/components/associationModal/associationModal.js

@@ -1,5 +1,116 @@
 Template.associationModal.events({
     'click #saveAssociations': function(e) {
-        log.info("Saving associations");
+        log.info('Saving associations');
+
+        // Close the modal
+        var saveButton = $(e.currentTarget);
+        saveButton.attr('disabled', true);
+        saveButton.addClass('btn-success').removeClass('btn-primary');
+
+        // Find the rows of the study association table
+        var tableRows = $('#studyAssociationTable table tbody tr');
+
+        // Create an empty object to group studies into
+        var studies = {};
+
+        // Loop through each row to parse the data
+        tableRows.each(function() {
+            // Get a selector for this row
+            var row = $(this);
+
+            // Check the includeStudy checkbox to see if we should parse this row
+            var includeStudy = row.find('input.includeStudy[type="checkbox"]').eq(0).prop('checked');
+            if (!includeStudy) {
+                return;
+            }
+
+            // Find the selected timepoint option for this study
+            var timepointInput = row.find('input.timepointOption[type="radio"]:checked');
+
+            // Find the related label and trim it down to actual label (TODO: do this another way)
+            var timepointType = timepointInput.val();
+
+            // Get the study metaData by checking the row with the template engine Blaze
+            var data = Blaze.getData(this);
+
+            // Concatenate the study data to an array, depending on whether is was marked as baseline
+            // or follow-up
+            if (!studies.hasOwnProperty(timepointType)) {
+                studies[timepointType] = [];
+            }
+
+            studies[timepointType].push(data);
+        });
+
+        Object.keys(studies).forEach(function(timepointType) {
+            // Get the studies associated with this timepoint
+            var relatedStudies = studies[timepointType];
+
+            // Create an array of all the studyInstanceUids for storage in the Timepoint
+            var studyInstanceUids = relatedStudies.map(function(study) {
+                return study.studyInstanceUid;
+            });
+
+            // Create an array of all the studyDates for storage in the Timepoint
+            var studyDates = relatedStudies.map(function(study) {
+                return moment(study.studyDate, 'YYYYMMDD');
+            });
+
+            // Sort the study dates, so we can get a range for these values
+            studyDates = studyDates.sort();
+
+            // Create a new timepoint to represent the (baseline or follow-up) studies
+            var timepoint = {
+                timepointType: timepointType,
+                timepointId: uuid.new(),
+                studyInstanceUids: studyInstanceUids,
+                patientId: relatedStudies[0].patientId, // TODO: Revisit this (Should timepoints be related to patientId?)
+                earliestDate: studyDates[0].format('YYYYMMDD'),
+                latestDate: studyDates[studyDates.length - 1].format('YYYYMMDD')
+            };
+
+            // Insert this timepoint into the Timepoints Collection
+            Timepoints.insert(timepoint);
+
+            // Loop through these studies to associate them with the newly created timepoint
+            relatedStudies.forEach(function(study) {
+                // Check if a study already exists in the Studies collection
+                var existingStudy = Studies.findOne({
+                    studyInstanceUid: study.studyInstanceUid
+                });
+
+                if (existingStudy) {
+                    // If a study already exists, update the entry with the new timepointId
+                    Studies.update(existingStudy._id, {
+                        $set: {
+                            timepointId: timepoint.timepointId
+                        }
+                    });
+                } else {
+                    // If no such study exists, update the entry with the new timepointId
+
+                    // Clear the ID from the document
+                    delete study._id;
+
+                    // Attach the timepointId and insert it into the Studies Collection
+                    study.timepointId = timepoint.timepointId;
+                    Studies.insert(study);
+                }
+            });
+        });
+
+        // Hide the modal
+        $('#associationModal').modal('hide');
+
+        // Reset the save button to its normal state
+        saveButton.removeClass('btn-success').addClass('btn-primary');
+        saveButton.attr('disabled', false);
+    },
+    'click #cancelAssociation': function() {
+        // When the modal is closed, we should reset
+        // the save button to its normal state
+        var saveButton = $('#saveAssociations');
+        saveButton.removeClass('btn-success').addClass('btn-primary');
+        saveButton.attr('disabled', false);
     }
 });

Packages/lesiontracker/client/components/conformanceCheckFeedback/conformanceCheckFeedback.html

@@ -0,0 +1,7 @@
+<template name="conformanceCheckFeedback">
+    <div id="conformanceCheckFeedback">
+        {{ #each validationErrors }}
+            <p data-toggle=""><i class="fa fa-exclamation-triangle fa-lg"></i> {{prefix}}{{error}}</p>
+        {{ /each }}
+    </div>
+</template>

Packages/lesiontracker/client/components/conformanceCheckFeedback/conformanceCheckFeedback.js

@@ -0,0 +1,11 @@
+Template.conformanceCheckFeedback.helpers({
+    validationErrors: function() {
+        // Return validation errors sorted by last added Target
+        return ValidationErrors.find({}, {
+            sort: {
+                prefix: -1,
+                type: 1
+            }
+        });
+    }
+});

Packages/lesiontracker/client/components/conformanceCheckFeedback/conformanceCheckFeedback.styl

@@ -0,0 +1,19 @@
+#conformanceCheckFeedback
+  position: absolute
+  right: 10px
+  color: darkorange
+  cursor: pointer
+  background: black
+
+  width: 30%
+  height: 30px
+  overflow: hidden
+
+  p
+    margin: 5px
+    text-align: center
+
+  &:hover
+    overflow: auto
+    height: 200px
+    z-index: 200

Packages/lesiontracker/client/components/lesionLocationDialog/lesionLocationDialog.js

@@ -11,24 +11,29 @@ function closeHandler(dialog) {
 
 // This event sets lesion number for new lesion
 function setLesionNumberCallback(measurementData, eventData, doneCallback) {
-    // Get the current element's timepointID from the study date metadata
+    // Get the current element's timepointId from the study date metadata
     var element = eventData.element;
     var enabledElement = cornerstone.getEnabledElement(element);
     var imageId = enabledElement.image.imageId;
 
     var study = cornerstoneTools.metaData.get('study', imageId);
+
+    // Find the relevant timepoint given the current study
     var timepoint = Timepoints.findOne({
-        timepointName: study.studyDate
+        studyInstanceUids: {
+            $in: [study.studyInstanceUid]
+        }
     });
+
     if (!timepoint) {
         return;
     }
 
-    measurementData.timepointID = timepoint.timepointID;
+    measurementData.timepointId = timepoint.timepointId;
 
     // Get a lesion number for this lesion, depending on whether or not the same lesion previously
     // exists at a different timepoint
-    var lesionNumber = LesionManager.getNewLesionNumber(measurementData.timepointID, isTarget = true);
+    var lesionNumber = LesionManager.getNewLesionNumber(measurementData.timepointId, isTarget = true);
     measurementData.lesionNumber = lesionNumber;
 
     // Set lesion number
@@ -226,6 +231,9 @@ Template.lesionLocationDialog.events({
             /// Set the isTarget value to true, since this is the target-lesion dialog callback
             measurementData.isTarget = true;
 
+            // Set the isNodal value based on the Location's properties
+            measurementData.isNodal = locationObj.isNodal;
+
             // Adds lesion data to timepoints array
             LesionManager.updateLesionData(measurementData);
         } else {
@@ -233,6 +241,7 @@ Template.lesionLocationDialog.events({
                 $set: {
                     location: locationObj.location,
                     locationId: locationObj.id,
+                    isNodal: locationObj.isNodal,
                     locationUID: id
                 }
             });

Packages/lesiontracker/client/components/lesionTableTimepointCell/lesionTableTimepointCell.js

@@ -5,18 +5,18 @@ Template.lesionTableTimepointCell.helpers({
         var lesionData = Template.parentData(1);
         return (lesionData &&
             lesionData.timepoints &&
-            lesionData.timepoints[this.timepointID]);
+            lesionData.timepoints[this.timepointId]);
     },
     displayData: function() {
         // Search Measurements by lesion and timepoint
         var lesionData = Template.parentData(1);
         if (!lesionData ||
             !lesionData.timepoints ||
-            !lesionData.timepoints[this.timepointID]) {
+            !lesionData.timepoints[this.timepointId]) {
             return;
         }
 
-        var data = lesionData.timepoints[this.timepointID];
+        var data = lesionData.timepoints[this.timepointId];
 
         if (lesionData.isTarget === true) {
             if (data.shortestDiameter) {
@@ -40,7 +40,7 @@ function doneCallback(measurementData, deleteTool) {
     // the specified Timepoint Cell
     if (deleteTool === true) {
         log.info('Confirm clicked!');
-        clearMeasurementTimepointData(measurementData.id, measurementData.timepointID);
+        clearMeasurementTimepointData(measurementData.id, measurementData.timepointId);
     }
 }
 
@@ -57,12 +57,12 @@ Template.lesionTableTimepointCell.events({
         var currentMeasurement = Template.parentData(1);
 
         // Create some fake measurement data
-        var currentTimepointID = this.timepointID;
+        var currentTimepointID = this.timepointId;
 
         var timepointData = currentMeasurement.timepoints[currentTimepointID];
         var measurementData = {
             id: currentMeasurement._id,
-            timepointID: currentTimepointID,
+            timepointId: currentTimepointID,
             response: timepointData.response,
             imageId: timepointData.imageId,
             handles: timepointData.handles,
@@ -83,7 +83,7 @@ Template.lesionTableTimepointCell.events({
         if (keyCode === keys.DELETE ||
             (keyCode === keys.D && e.ctrlKey === true)) {
             var currentMeasurement = Template.parentData(1);
-            var currentTimepointID = this.timepointID;
+            var currentTimepointID = this.timepointId;
 
             showConfirmDialog(function() {
                 clearMeasurementTimepointData(currentMeasurement._id, currentTimepointID);

Packages/lesiontracker/client/components/lesionTableTimepointHeader/lesionTableTimepointHeader.html

@@ -1,9 +1,6 @@
 <template name="lesionTableTimepointHeader">
-    <th class="lesionTableTimepointCell">
+    <th class="lesionTableTimepointCell" title="Latest study date: {{formatDA latestDate "MM/DD/YYYY"}}"
-        {{formatDA timepointName "MM/DD/YYYY"}}
+        data-toggle="tooltip" data-placement="top">
-        {{#if timepointTextFound}}
+        {{ timepointName }}
-            {{timepointText}}
-        {{/if}}
-        {{#if timepointLoaded }}<span class="timepointIndicator">&lt;</span> {{/if}}
     </th>
 </template>

Packages/lesiontracker/client/components/lesionTableTimepointHeader/lesionTableTimepointHeader.js

@@ -1,105 +1,6 @@
-Template.lesionTableTimepointHeader.events({
-    'click th.lesionTableTimepointCell': function(e, template) {
-        var parentPosition = getPosition(e.currentTarget);
-        var cellText = e.currentTarget.innerText;
-
-        // Remove spaces in string
-        cellText = cellText.replace(/\s/g, ''); // Remove spaces
-        cellText = cellText.replace('<', ''); // Remove <
-        var splitCellText = cellText.split('/');
-        var dateStr = splitCellText[2].replace(/\D/g,'') + '' + splitCellText[0].replace(/\D/g,'') + '' + splitCellText[1].replace(/\D/g,''); // Remove non-digit chars
-
-        // Check patient has a timepointText as Baseline
-        var patientId = template.data.patientId;
-
-        // Open popup
-        var timepointTextDialog = $('#timepointTextDialog');
-        var dialogDisplay = timepointTextDialog.css('display');
-        if (dialogDisplay === 'none') {
-            var isBaselineInCollection = Timepoints.findOne({
-                patientId: patientId,
-                timepointName: dateStr,
-                timepointText: 'Baseline'
-            });
-
-            // If isBaselineInCollection is true, "Baseline" is found in collection for patient and set checkbox as checked
-            if (isBaselineInCollection) {
-                // Set checkbox as checked
-                $('#checkBoxBaseline').prop('checked', true);
-            } else {
-                // Set checkbox as unchecked
-                $('#checkBoxBaseline').prop('checked', false);
-            }
-
-            // Open dialog
-            var dialogProperty = {
-                top: parentPosition.y - 30,
-                left: parentPosition.x,
-                display: 'block'
-            };
-
-            timepointTextDialog.css(dialogProperty);
-        } else {
-            // Get timepoints of patient
-            // Set timepointText as Baseline for selected timepoint
-            var timepoints = Timepoints.find({
-                patientId: patientId
-            }).fetch();
-
-            // Check checkbox is selected
-            var checkboxBaselineChecked = $('#checkBoxBaseline').is(':checked');
-
-            timepoints.forEach(function(timepoint) {
-                // timepointText defines a custom text for timepoint such as Baseline, Nadir, Current
-                if (timepoint.timepointName === dateStr) {
-                    // If checkbox is selected, set timepointText as Baseline
-                    // Else set timepointText as ""
-                    var timepointText = 'Baseline';
-                    if (!checkboxBaselineChecked) {
-                        timepointText = '';
-                    }
-
-                    Timepoints.update(timepoint._id,{
-                        $set: {
-                            timepointText: timepointText
-                        }
-                    });
-                } else {
-                    // Set timepointText as empty
-                    Timepoints.update(timepoint._id,{
-                        $set: {
-                            timepointText: ''
-                        }
-                    });
-                }
-            });
-
-            // Close dialog
-            timepointTextDialog.css('display', 'none');
-        }
-    }
-});
-
 Template.lesionTableTimepointHeader.helpers({
-    timepointTextFound: function() {
+    'timepointName': function() {
-        var timepointText = this.timepointText;
+        var timepoint = this;
-        return (timepointText && timepointText === 'Baseline');
+        return getTimepointName(timepoint);
     }
 });
-
-// Gets parent's position of element which mouse pointer is clicked in
-function getPosition(element) {
-    var xPosition = 0;
-    var yPosition = 0;
-
-    while (element) {
-        xPosition += (element.offsetLeft - element.scrollLeft + element.clientLeft);
-        yPosition += (element.offsetTop - element.scrollTop + element.clientTop);
-        element = element.offsetParent;
-    }
-
-    return {
-        x: xPosition,
-        y: yPosition
-    };
-}

Packages/lesiontracker/client/components/lesionTrackerLayout/lesionTrackerLayout.html

@@ -1,9 +1,10 @@
-<template name="layoutLesionTracker">
+<template name="lesionTrackerLayout">
     <div class="logoContainer">
         <a class="navbar-brand" href="http://ohif.org">
             <img src="/images/logo.png">
             <h4 class="name">Open Health Imaging Foundation</h4>
         </a>
     </div>
-    {{> yield}}
+    {{ >optionsButton }}
+    {{ >yield }}
 </template>

Packages/lesiontracker/client/components/lesionTrackerViewportOverlay/lesionTrackerViewportOverlay.html

@@ -0,0 +1,26 @@
+<template name="lesionTrackerViewportOverlay">
+    <div class="imageViewerViewportOverlay noselect">
+        <div class="topleft dicomTag">
+            <div>{{formatPN patientName}}</div>
+            <div>{{patientId}}</div>
+            <div class='timepointName'>{{timepointName}}</div>
+        </div>
+        <div class="topright dicomTag">
+            <div>{{studyDescription}}</div>
+            <div>{{formatDA studyDate}} {{formatTM studyTime}}</div>
+        </div>
+        <div class="bottomright dicomTag">
+            <div>Zoom: {{formatNumberPrecision zoom 2}}%</div>
+            <div>{{compression}}</div>
+            <div>{{wwwc}}</div>
+        </div>
+        <div class="bottomleft dicomTag">
+            <div>Ser: {{seriesNumber}}</div>
+            <div>Img: {{imageNumber}} ({{imageIndex}}/{{numImages}})</div>
+            <div>{{frameRate}}</div>
+            <div>{{imageDimensions}}</div>
+            <div>{{seriesDescription}}</div>
+        </div>
+        {{>imageControls}}
+    </div>
+</template>

Packages/lesiontracker/client/components/lesionTrackerViewportOverlay/lesionTrackerViewportOverlay.js

@@ -0,0 +1,30 @@
+// Use Aldeed's meteor-template-extension package to replace the
+// default viewportOverlay template.
+// See https://github.com/aldeed/meteor-template-extension
+var defaultTemplate = 'viewportOverlay';
+Template.lesionTrackerViewportOverlay.replaces(defaultTemplate);
+
+// Add the TimepointName helper to the default template. The
+// HTML of this template is replaced with that of lesionTrackerViewportOverlay
+Template[defaultTemplate].helpers({
+    timepointName: function() {
+        var data = this;
+        var study = Studies.findOne({
+            studyInstanceUid: data.studyInstanceUid
+        });
+
+        if (!study) {
+            return;
+        }
+
+        var timepoint = Timepoints.findOne({
+            timepointId: study.timepointId
+        });
+
+        if (!timepoint) {
+            return;
+        }
+
+        return getTimepointName(timepoint);
+    }
+});

Packages/lesiontracker/client/components/lesionTrackerViewportOverlay/lesionTrackerViewportOverlay.styl

@@ -0,0 +1,3 @@
+.imageViewerViewportOverlay
+  .timepointName
+    color: #32BFFF

Packages/lesiontracker/client/components/lesionTrackerWorklistContextMenu/lesionTrackerWorklistContextMenu.html

@@ -1,11 +1,10 @@
-<template name="studyContextMenu">
+<template name="lesionTrackerWorklistContextMenu">
     <div id="studyContextMenu" class="studyContextMenu noselect"
          oncontextmenu='return false;'
          unselectable='on'
          onselectstart='return false;'>
         <ul>
             <li>
-                <!--<a id="deleteTool">Delete</a>-->
                 <!-- TODO: Make this dynamically accept options-->
                 <a id="launchStudyAssociation" type="button"
                    data-toggle="modal"
@@ -14,16 +13,20 @@
                     <i class="fa fa-calendar-plus-o fa-lg"></i>
                     Associate
                 </a>
-                <a><span class="fa-stack fa-lg">
+                <a id="removeTimepointAssociations" type="button"
+                    title="Remove Timepoint Association">
+                    <i class="fa fa-eraser fa-lg"></i> Remove Association
+                </a>
+                <a class="disabled"><span class="fa-stack fa-lg">
                       <i class="fa fa-user fa-stack-1x"></i>
                       <i class="fa fa-ban fa-stack-2x text-danger"></i>
                     </span> Anonymize
                 </a>
-                <a><i class="fa fa-trash fa-lg"></i> Delete</a>
+                <a class="disabled"><i class="fa fa-trash fa-lg"></i> Delete</a>
-                <a><i class="fa fa-send-o fa-lg"></i> Send</a>
+                <a class="disabled"><i class="fa fa-send-o fa-lg"></i> Send</a>
-                <a><i class="fa fa-exchange fa-lg"></i> Export</a>
+                <a class="disabled"><i class="fa fa-exchange fa-lg"></i> Export</a>
-                <a><i class="fa fa-download fa-lg"></i> Download</a>
+                <a class="disabled"><i class="fa fa-download fa-lg"></i> Download</a>
-                <a><i class="fa fa-photo fa-lg"></i> View Series Details</a>
+                <a class="disabled"><i class="fa fa-photo fa-lg"></i> View Series Details</a>
             </li>
         </ul>
     </div>

Packages/lesiontracker/client/components/lesionTrackerWorklistContextMenu/lesionTrackerWorklistContextMenu.js

@@ -0,0 +1,75 @@
+// Use Aldeed's meteor-template-extension package to replace the
+// default WorklistStudy template.
+// See https://github.com/aldeed/meteor-template-extension
+var defaultTemplate = 'studyContextMenu';
+Template.lesionTrackerWorklistContextMenu.replaces(defaultTemplate);
+
+Worklist.functions['removeTimepointAssociations'] = removeTimepointAssociations;
+
+/**
+ * Removes all present study / timepoint associations from the Clinical Trial
+ */
+function removeTimepointAssociations() {
+    // Get a Cursor pointing to the selected Studies from the Worklist
+    var selectedStudies = WorklistSelectedStudies.find({}, {
+        sort: {
+            studyDate: 1
+        }
+    });
+
+    // Loop through the Cursor of Selected Studies
+    selectedStudies.forEach(function(selectedStudy) {
+        // Find the selected study in question in the Collection of
+        // Timepoint/Study associated Studies
+        var study = Studies.findOne({
+            studyInstanceUid: selectedStudy.studyInstanceUid
+        });
+
+        // If the studies that were selected are not already associated
+        // with a Timepoint, stop here
+        if (!study) {
+            return;
+        }
+
+        // Update the Studies Collection to remove the link to this Timepoint
+        Studies.update(study._id, {
+            unset: {
+                timepointId: ''
+            }
+        });
+
+        // Find the Timepoint that was previously referenced
+        var timepoint = Timepoints.findOne({
+            timepointId: study.timepointId
+        });
+
+        // Find the index of the current studyInstanceUid in the array
+        // of reference studyInstanceUids
+        var index = timepoint.studyInstanceUids.indexOf(study.studyInstanceUid);
+        if (index < 0) {
+            return;
+        }
+
+        // Remove the specified studyInstanceUid from the array of associated studyInstanceUids
+        timepoint.studyInstanceUids.splice(index, 1);
+
+        // Check if there are still one or more Studies associated with this Timepoint
+        if (timepoint.studyInstanceUids.length) {
+            // Update the Timepoints Collection with this modified array for the
+            // studyInstanceUids attribute
+            Timepoints.update(timepoint._id, {
+                $set: {
+                    studyInstanceUids: timepoint.studyInstanceUids
+                }
+            });
+        } else {
+            // If no more Studies are associated with this Timepoint, we should remove it
+            // from the Timepoints Collection via a server call
+            Meteor.call('removeTimepoint', timepoint._id, function(error) {
+                if (error) {
+                    log.warn(error);
+                }
+            });
+        }
+    });
+}

Packages/lesiontracker/client/components/lesionTrackerWorklistStudy/lesionTrackerWorklistStudy.html

@@ -0,0 +1,31 @@
+<template name="lesionTrackerWorklistStudy">
+    <tr class="worklistStudy noselect">
+        <td>
+            {{formatPN patientName}}
+        </td>
+        <td>
+            {{patientId}}
+        </td>
+        {{#unless isTouchDevice}}
+        <td>
+            {{accessionNumber}}
+        </td>
+        {{/unless}}
+        <td>
+            {{formatDA studyDate}} {{ #if timepointName }}({{timepointName}}){{ /if }}
+        </td>
+        {{#unless isTouchDevice}}
+        <td>
+            {{modalities}}
+        </td>
+        {{/unless}}
+        <td>
+            {{studyDescription}}
+        </td>
+        {{#unless isTouchDevice}}
+        <td>
+            {{numberOfStudyRelatedInstances}}
+        </td>
+        {{/unless}}
+    </tr>
+</template>

Packages/lesiontracker/client/components/lesionTrackerWorklistStudy/lesionTrackerWorklistStudy.js

@@ -0,0 +1,30 @@
+// Use Aldeed's meteor-template-extension package to replace the
+// default WorklistStudy template.
+// See https://github.com/aldeed/meteor-template-extension
+var defaultTemplate = 'worklistStudy';
+Template.lesionTrackerWorklistStudy.replaces(defaultTemplate);
+
+// Add the TimepointName helper to the default template. The
+// HTML of this template is replaced with that of lesionTrackerWorklistStudy
+Template[defaultTemplate].helpers({
+    timepointName: function() {
+        var data = this;
+        var study = Studies.findOne({
+            studyInstanceUid: data.studyInstanceUid
+        });
+
+        if (!study) {
+            return;
+        }
+
+        var timepoint = Timepoints.findOne({
+            timepointId: study.timepointId
+        });
+
+        if (!timepoint) {
+            return;
+        }
+
+        return getTimepointName(timepoint);
+    }
+});

Packages/lesiontracker/client/components/nonTargetLesionDialog/nonTargetLesionDialog.js

@@ -11,24 +11,29 @@ function closeHandler(dialog) {
 
 // This event sets lesion number for new lesion
 function setLesionNumberCallback(measurementData, eventData, doneCallback) {
-    // Get the current element's timepointID from the study date metadata
+    // Get the current element's timepointId from the study date metadata
     var element = eventData.element;
     var enabledElement = cornerstone.getEnabledElement(element);
     var imageId = enabledElement.image.imageId;
 
     var study = cornerstoneTools.metaData.get('study', imageId);
+
+    // Find the relevant timepoint given the current study
     var timepoint = Timepoints.findOne({
-        timepointName: study.studyDate
+        studyInstanceUids: {
+            $in: [study.studyInstanceUid]
+        }
     });
+
     if (!timepoint) {
         return;
     }
 
-    measurementData.timepointID = timepoint.timepointID;
+    measurementData.timepointId = timepoint.timepointId;
 
     // Get a lesion number for this lesion, depending on whether or not the same lesion previously
     // exists at a different timepoint
-    var lesionNumber = LesionManager.getNewLesionNumber(measurementData.timepointID, isTarget = false);
+    var lesionNumber = LesionManager.getNewLesionNumber(measurementData.timepointId, isTarget = false);
     measurementData.lesionNumber = lesionNumber;
 
     // Set lesion number
@@ -211,7 +216,7 @@ changeNonTargetLocationCallback = function(measurementData, eventData, doneCallb
             multi: true
         });
 
-    var response = measurement.timepoints[measurementData.timepointID].response;
+    var response = measurement.timepoints[measurementData.timepointId].response;
 
     // TODO = Standardize this. Searching by code probably isn't the best, we should use
     // some sort of UID

Packages/lesiontracker/client/components/nonTargetResponseDialog/nonTargetResponseDialog.js

@@ -65,7 +65,7 @@ changeNonTargetResponse = function(measurementData, eventData, doneCallback) {
         return;
     }
 
-    var response = measurement.timepoints[measurementData.timepointID].response;
+    var response = measurement.timepoints[measurementData.timepointId].response;
 
     // TODO = Standardize this. Searching by code probably isn't the best, we should use
     // some sort of UID

Packages/lesiontracker/client/components/optionsButton/optionsButton.html

@@ -0,0 +1,12 @@
+<template name="optionsButton">
+    <div class="optionsButton">
+        <a type="button"
+           class="btn btn-default"
+           data-toggle="modal"
+           data-target="#optionsModal"
+           title="Trial Options">
+            <i class="fa fa-cog fa-lg"></i>
+            Trial Options
+        </a>
+    </div>
+</template>

Packages/lesiontracker/client/components/optionsButton/optionsButton.styl

@@ -0,0 +1,6 @@
+// These settings are temporary!
+.optionsButton
+  position: absolute
+  top: 3px
+  right: 350px
+  cursor: pointer

Packages/lesiontracker/client/components/optionsModal/optionsModal.html

@@ -0,0 +1,83 @@
+<template name="optionsModal">
+    <div class="modal" id="optionsModal" tabindex="-1" role="dialog" aria-labelledby="optionsModalLabel">
+        <div class="modal-dialog modal-lg" role="document">
+            <div class="modal-content">
+                <div class="modal-header">
+                    <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+                    <h4 class="modal-title" id="optionsModalLabel">Clinical Trial Options</h4>
+                </div>
+                <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>
+                            </div>
+                        </div>
+                    </div>
+                    <br/>
+                    <div class="row">
+                        <div class="col-md-12">
+                            <h4>Additional Options</h4>
+                            <a type="button" class="btn btn-danger clearAllStudyTimepointAssociations">
+                                <i class="fa fa-trash"></i> Clear All Study/Timepoint Associations
+                            </a>
+                        </div>
+                    </div>
+                </div>
+                <div class="modal-footer">
+                    <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+                </div>
+            </div>
+        </div>
+    </div>
+</template>

Packages/lesiontracker/client/components/optionsModal/optionsModal.js

@@ -0,0 +1,33 @@
+Session.setDefault('TrialResponseAssessmentCriteria', 'RECIST');
+
+Template.optionsModal.events({
+    /**
+     * When the trial criteria radio buttons are changed, change the
+     * trial assessment criteria for the Lesion Tracker
+     *
+     * @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();
+
+        // 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);
+
+        log.info('Trial Criteria changed to: ' + criteriaType);
+    },
+    /**
+     * When the Clear Study/Timepoint Associations button is clicked, we
+     * send a call to the server to erase all entries in the Timepoints Collection.
+     */
+    'click a.clearAllStudyTimepointAssociations': function() {
+        Meteor.call('clearAllTimepoints', function(error) {
+            if (error) {
+                log.warn(error);
+            }
+        });
+    }
+});

Packages/lesiontracker/client/components/optionsModal/optionsModal.styl

@@ -0,0 +1,2 @@
+.trialCriteriaLabel
+  margin: 0 5px

Packages/lesiontracker/client/components/studyAssociationTable/studyAssociationTable.html

@@ -43,13 +43,15 @@
                     <td class="studyDataCell {{ #if autoselected }}disabled{{ /if }}">
                         <p>{{studyDescription}}</p>
                     </td>
-                    <td class="timepointOptions center studyDataCell {{ #if autoselected }}disabled{{ /if }}">
+                    <td class="timepointOptions center studyDataCell noselect {{ #if autoselected }}disabled{{ /if }}">
                         {{ #each timepointOptions }}
-                            <label>
+                            <label class="noselect">
                                 <input type="radio"
                                       name="{{../_id}}"
-                                          value={{type}}
+                                      value="{{value}}"
-                                          {{ inlineIf autoselected true 'disabled'}}>
+                                      class="timepointOption"
+                                      {{ inlineIf checked true 'checked' }}
+                                      {{ inlineIf autoselected true 'disabled' }}>
                                     {{name}}
                             </label>
                         {{ /each }}

Packages/lesiontracker/client/components/studyAssociationTable/studyAssociationTable.js

@@ -30,8 +30,13 @@ function getDateRange(selectedStudies, range) {
 }
 
 /**
+ * Selects all studies related to the currently input studies,
+ * based on various criteria. Returns the entire array of related studies.
  *
- * @returns {Array}
+ * (at the moment, this is only the date range +/- 14 days, with a matching patientId)
+ *
+ * @param selectedStudies A user-selected list of studies
+ * @returns {*} The entire array of related studies
  */
 function autoSelectStudies(selectedStudies) {
     if (!selectedStudies.length) {
@@ -40,6 +45,9 @@ function autoSelectStudies(selectedStudies) {
 
     var range = getDateRange(selectedStudies);
 
+    // Fetch autoselected studies based on the date range
+    // Note that we used MongoDB's fetch here so we have a mutable array,
+    // rather than a Cursor
     var autoselected = WorklistStudies.find({
         studyDate: {
             $gte: range.earliestDate.format('YYYYMMDD'),
@@ -82,8 +90,8 @@ Template.studyAssociationTable.helpers({
                     studyDate: 1
                 }
             }).fetch() || [];
-        var autoselected = autoSelectStudies(selectedStudies);
+
-        return autoselected;
+        return autoSelectStudies(selectedStudies);
     },
     /**
      * This helper returns the list of Timepoint types the user can set for this study
@@ -91,16 +99,15 @@ Template.studyAssociationTable.helpers({
      * @returns {Array.<T>}
      */
     timepointOptions: function() {
-        return [
+        return [{
-            {
                 value: 'baseline',
-                name: 'Baseline'
+                name: 'Baseline',
-            },
+                checked: true
-            {
+            }, {
                 value: 'followup',
-                name: 'Follow-up'
+                name: 'Follow-up',
-            }
+                checked: false
-        ];
+            }];
     },
     earliestDate: function() {
         var selectedStudies = WorklistSelectedStudies.find({}, {
@@ -108,12 +115,11 @@ Template.studyAssociationTable.helpers({
                 studyDate: 1
             }
         }).fetch();
-        var range = getDateRange(selectedStudies);
-        if (!range) {
-            return;
-        }
 
+        var range = getDateRange(selectedStudies);
+        if (range) {
             return range.earliestDate;
+        }
     },
     latestDate: function() {
         var selectedStudies = WorklistSelectedStudies.find({}, {
@@ -121,13 +127,12 @@ Template.studyAssociationTable.helpers({
                 studyDate: 1
             }
         }).fetch();
-        var range = getDateRange(selectedStudies);
-        if (!range) {
-            return;
-        }
 
+        var range = getDateRange(selectedStudies);
+        if (range) {
             return range.latestDate;
         }
+    }
 });
 
 Template.studyAssociationTable.events({
@@ -143,12 +148,3 @@ Template.studyAssociationTable.events({
         }
     }
 });
-
-//trial criteria!
-/*There shall be Associate option in right-click dialog
-If associated, double-click shall go to image view.
-    If not associated, user shall be directed to Associate Time Points Dialog
-Use shall also be allowed to select multiple studies from study list to associate
-Associate Time Point dialog shall present selected studies and studies within defined time window of =/- 14 days of selected studies
-User should only be able to associate one time point at a time (user should not be able to select both BL and F/U for different studies in associate dialog)
-   */

Packages/lesiontracker/client/components/studyDateList/studyDateList.html

@@ -4,7 +4,7 @@
         <span class="loading"><i class="fa fa-spinner fa-spin"></i></span>
         <select id="selectStudyDate">
             {{#each relatedStudies}}
-                <option value="{{studyInstanceUid}}" selected={{selected}}>{{formatDA studyDate}}</option>
+                <option value="{{studyInstanceUid}}" selected={{selected}}>{{formatDA studyDate}} ({{timepointName}})</option>
             {{/each}}
         </select>
     </div>

Packages/lesiontracker/client/components/studyDateList/studyDateList.js

@@ -4,21 +4,22 @@ Template.studyDateList.helpers({
      * The value for 'selected' for the currently loaded study is set to true, so that
      * this becomes the current option in the combo box.
      *
-     * @returns {*}
+     * @returns {*} Array of studies that are related to the current study by patient ID
      */
     relatedStudies: function() {
-        // TODO= Fix this! This won't work to retrieve all studies
-        // related to this patient. We will need to do a real search
-        // since the WorklistStudies Collection only contains the studies on-screen
-
         // Check which study is currently loaded into the study browser
         var currentStudyInBrowser = ViewerStudies.findOne({
             selected: true
         });
 
-        // Find studies which have the same patientId as the currently selected study
+        // Find all Timepoint-associated studies which have the same patientId as the currently selected study
-        var relatedStudies = WorklistStudies.find({patientId: currentStudyInBrowser.patientId},
+        var relatedStudies = Studies.find({
-                {sort: {studyDate: 1}}).fetch();
+            patientId: currentStudyInBrowser.patientId
+        }, {
+            sort: {
+                studyDate: 1
+            }
+        });
 
         // Modify the array of related studies so the default option is the currently selected study
         relatedStudies.forEach(function(study) {
@@ -31,6 +32,26 @@ Template.studyDateList.helpers({
 
         // Use this array to populate the combo box
         return relatedStudies;
+    },
+    timepointName: function() {
+        var data = this;
+        var study = Studies.findOne({
+            studyInstanceUid: data.studyInstanceUid
+        });
+
+        if (!study) {
+            return;
+        }
+
+        var timepoint = Timepoints.findOne({
+            timepointId: study.timepointId
+        });
+
+        if (!timepoint) {
+            return;
+        }
+
+        return getTimepointName(timepoint);
     }
 });
 
@@ -46,7 +67,6 @@ Template.studyDateList.events({
      */
     'change select#selectStudyDate': function(e) {
         var selectBox = $(e.currentTarget);
-
         var studyInstanceUid = selectBox.val();
 
         // Hide the select box
@@ -57,6 +77,11 @@ Template.studyDateList.events({
         loadingIndicator.css('display', 'block');
 
         Meteor.call('GetStudyMetadata', studyInstanceUid, function(error, study) {
+            if (error) {
+                log.warn(error);
+                return;
+            }
+
             sortStudy(study);
 
             // Hide the loading indicator
@@ -66,13 +91,11 @@ Template.studyDateList.events({
             selectBox.css('display', 'block');
 
             // Set "Selected" to false for the entire collection
-            ViewerStudies.update({},
+            ViewerStudies.update({}, {
-                {
                 $set: {
                     selected: false
                 }
-                },
+            }, {
-                {
                 multi: true
             });
 
@@ -81,6 +104,7 @@ Template.studyDateList.events({
             var existingStudy = ViewerStudies.findOne({
                 studyInstanceUid: studyInstanceUid
             });
+
             if (existingStudy) {
                 // Set the current finding in the collection to true
                 ViewerStudies.update(existingStudy._id, {
@@ -95,29 +119,6 @@ Template.studyDateList.events({
             // with the value True, and insert it into the ViewerStudies Collection
             study.selected = true;
             ViewerStudies.insert(study);
-
-            var timepointID = uuid.v4();
-
-            var timepoint = Timepoints.findOne({
-                timepointName: study.studyDate
-            });
-            if (timepoint) {
-                log.warn('A timepoint with that study date already exists!');
-                return;
-            }
-
-            var testTimepoint = Timepoints.findOne({});
-            if (testTimepoint && testTimepoint.patientId !== study.patientId) {
-                log.warn('Timepoints collection related to the wrong subject');
-                return;
-            }
-
-            log.info('Inserting a new timepoint');
-            Timepoints.insert({
-                patientId: study.patientId,
-                timepointID: timepointID,
-                timepointName: study.studyDate
-            });
         });
     }
 });

Packages/lesiontracker/lib/LesionManager.js

@@ -0,0 +1,202 @@
+/**
+ * Retrieve a location name (e.g. Liver Right) from the
+ * PatientLocations Collection by id, if it exists. Otherwise,
+ * return an empty string.
+ *
+ * @param id
+ * @returns {*|string}
+ */
+function getLocationName(id) {
+    var locationObject = PatientLocations.findOne(id);
+    if (!locationObject || !locationObject.location) {
+        return '';
+    }
+
+    return locationObject.location;
+}
+
+/**
+ * Update the Timepoint object for a specific Measurement.
+ * If no measurement exists yet, one will be created.
+ *
+ * Input is toolData from the lesion or nonTarget tool
+ *
+ * @param lesionData
+ */
+function updateLesionData(lesionData) {
+    var study = Studies.findOne({
+        studyInstanceUid: lesionData.studyInstanceUid
+    });
+
+    if (!study) {
+        log.warn('Study is not associated with a timepoint');
+        return;
+    }
+
+
+    var timepoint = Timepoints.findOne({
+        timepointId: study.timepointId
+    });
+
+    if (!timepoint) {
+        log.warn('Timepoint in an image is not present in the Timepoints Collection?');
+        return;
+    }
+
+    // Find the specific lesion to be updated
+    var existingMeasurement;
+    if (lesionData.id && lesionData.id !== 'notready') {
+        existingMeasurement = Measurements.findOne(lesionData.id);
+    } else {
+        existingMeasurement = Measurements.findOne({
+            lesionNumber: lesionData.lesionNumber,
+            isTarget: lesionData.isTarget
+        });
+    }
+
+    // Create a structure for the timepointData based
+    // on this Lesion's toolData
+    var timepointData = {
+        seriesInstanceUid: lesionData.seriesInstanceUid,
+        studyInstanceUid: lesionData.studyInstanceUid,
+        sopInstanceUid: lesionData.sopInstanceUid,
+        handles: lesionData.handles,
+        imageId: lesionData.imageId
+    };
+
+    if (lesionData.isTarget === true) {
+        timepointData.shortestDiameter = lesionData.widthMeasurement;
+        timepointData.longestDiameter = lesionData.measurementText;
+    } else {
+        timepointData.response = lesionData.response;
+    }
+
+    // If no such lesion exists, we need to add one
+    if (!existingMeasurement) {
+        // Create a data structure for the Measurement
+        // based on the current tool data
+        var measurement = {
+            lesionNumber: lesionData.lesionNumber,
+            isTarget: lesionData.isTarget,
+            patientId: lesionData.patientId,
+            id: lesionData.id
+        };
+
+        // Retrieve the location name given the locationUID
+        if (lesionData.locationUID !== undefined) {
+            var locationObj = PatientLocations.findOne({
+                locationUID: lesionData.locationUID
+            });
+
+            measurement.location = locationObj.location;
+            measurement.isNodal = locationObj.isNodal;
+        }
+
+        // Add toolData parameters to the Measurement at this Timepoint
+        measurement.timepoints = {};
+        measurement.timepoints[timepoint.timepointId] = timepointData;
+
+        // Set a flag to prevent duplication of toolData
+        measurement.toolDataInsertedManually = true;
+
+        // Increment and store the absolute Lesion Number for this Measurement
+        measurement.lesionNumberAbsolute = Measurements.find().count() + 1;
+
+        // Insert this into the Measurements Collection
+        // Save the ID into the toolData (not sure if this works?)
+        measurement.id = Measurements.insert(measurement);
+
+        // Update the database entry so it can be readded next time the study is loaded
+        Measurements.update(measurement.id, {
+            $set: {
+                toolDataInsertedManually: false
+            }
+        });
+    } else {
+        lesionData.id = existingMeasurement._id;
+        lesionData.isNodal = existingMeasurement.isNodal;
+
+        // Update timepoints from lesion data
+        existingMeasurement.timepoints[timepoint.timepointId] = timepointData;
+
+        Measurements.update(existingMeasurement._id, {
+            $set: {
+                timepoints: existingMeasurement.timepoints
+            }
+        });
+    }
+}
+
+/**
+ * Returns new lesion number according to timepointId
+ * @param timepointId
+ * @param isTarget
+ * @returns {*}
+ */
+function getNewLesionNumber(timepointId, isTarget) {
+    // Get all current lesion measurements
+    var numMeasurements = Measurements.find({
+        isTarget: isTarget
+    }).count();
+
+    // If no measurements exist yet, start at 1
+    if (!numMeasurements) {
+        return 1;
+    }
+
+    // Find related measurements (i.e. target or non-target)
+    var measurements = Measurements.find({
+        isTarget: isTarget
+    }, {
+        sort: {
+            lesionNumber: 1
+        }
+    }).fetch();
+
+    // If measurements exist, find the last lesion number
+    // from the given timepoint
+    var lesionNumberCounter = 1;
+
+    // Search through every Measurement to see which ones
+    // already have data for this Timepoint, if we find one that
+    // doesn't have data, we will stop there and use that as the
+    // current Measurement
+    measurements.every(function(measurement) {
+        // If this measurement has no data for this Timepoint,
+        // use this as the current Measurement
+        if (!measurement.timepoints[timepointId]) {
+            lesionNumberCounter = measurement.lesionNumber;
+            return false;
+        }
+
+        lesionNumberCounter++;
+        return true;
+    });
+    return lesionNumberCounter;
+}
+
+/**
+ * If the current Lesion Number already exists
+ * for any other timepoint, returns lesion locationUID
+ * @param lesionData
+ * @returns {*}
+ */
+function lesionNumberExists(lesionData) {
+    var measurement = Measurements.findOne({
+        lesionNumber: lesionData.lesionNumber,
+        isTarget: lesionData.isTarget
+    });
+
+    if (!measurement) {
+        return;
+    }
+
+    return measurement.locationUID;
+}
+
+LesionManager = {
+    updateLesionData: updateLesionData,
+    getNewLesionNumber: getNewLesionNumber,
+    lesionNumberExists: lesionNumberExists,
+    getLocationName: getLocationName
+};

Packages/lesiontracker/lib/TrialCriteriaConstraints.js

@@ -0,0 +1,388 @@
+// Define the Trial Criteria Structure
+TrialCriteriaConstraints = {
+    RECIST: RECIST,
+    irRC: irRC
+};
+
+/**
+ * RECIST 1.1 Trial Criteria Definition
+ *
+ * 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)
+ * - Time Point Measurement Total = Sum of long axis measurements for extranodal target lesion + short axis measurements for nodal lesions
+ */
+function RECIST(image) {
+    var acquisitionSliceThickness;
+    if (image) {
+        acquisitionSliceThickness = image.acquisitionSliceThickness;
+
+        // TODO: Use metaData to determine if this is a chest X-ray
+        var isChestXray = false;
+    }
+
+    // Define the RECIST 1.1 structure
+    var criteria = {
+        baseline: {
+            target: {},
+            nonTarget: {},
+            group: {}
+        }
+    };
+
+    if (acquisitionSliceThickness) {
+        criteria.baseline.target.nodal = {
+            shortestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: Math.min(15, 2 * acquisitionSliceThickness),
+                    message: '^Nodal lesions must be >= 15 mm short axis AND >= double the acquisition slice thickness (' +
+                             acquisitionSliceThickness + ' mm) for CT and MR.'
+                }
+            }
+        };
+    } else {
+        criteria.baseline.target.nodal = {
+            shortestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: 15,
+                    message: '^Nodal target lesions must be >= %{count} mm short axis'
+                }
+            }
+        };
+    }
+
+    criteria.baseline.target.all = {
+        // - Target lesions must have measurements (cannot be assessed as CR, UN/NE, EX)
+        response: {
+            exclusion: {
+                within: {
+                    CR: 'Complete Response (CR)',
+                    UN: 'Unknown (UN)',
+                    NE: 'Non-evaluable (NE)',
+                    EX: 'Excluded (EX)'
+                },
+                message: '^Target lesions must have a length and cannot be marked as %{value} at baseline.'
+            }
+        },
+        totalLesionBurden: {
+            numericality: {
+                greaterThanOrEqualTo: 2, // TODO: Check this, the value wasn't specified!
+                message: '^Total lesion burden (SPD target lesions + SPD new lesions) should be greater than %{count}.'
+            }
+        }
+    };
+
+    criteria.baseline.nonTarget.all = {
+        // - Non-targets can only be assessed as 'present'
+        response: {
+            // This is a workaround since Validating equality to something is not implemented yet
+            // https://github.com/ansman/validate.js/issues/79
+            presence: {
+                message: "^Non-target lesions can only be assessed as 'Present' at Baseline"
+            },
+            inclusion: {
+                within: ['Present'],
+                message: "^Non-target lesions can only be assessed as 'Present' at Baseline"
+            }
+        }
+    };
+
+    criteria.baseline.perOrgan = {
+        numberOfLesionsPerOrgan: {
+            numericality: {
+                lessThanOrEqualTo: 2,
+                //message: '^A maximum of %{count} target lesions per organ are allowed at Baseline.'
+            }
+        }
+    };
+
+    criteria.baseline.group = {
+        totalNumberOfLesions: {
+            numericality: {
+                lessThanOrEqualTo: 5,
+                //message: '^A maximum of %{count} target lesions total are allowed at Baseline.'
+            }
+        }
+    };
+
+    if (acquisitionSliceThickness) {
+        criteria.baseline.target.extraNodal = {
+            longestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: Math.min(10, 2 * acquisitionSliceThickness),
+                    message: '^Extranodal lesions must be >= 10 mm long axis AND >= double the acquisition slice thickness (' +
+                    acquisitionSliceThickness + ' mm) for CT and MR.'
+                }
+            }
+        };
+    } else if (isChestXray) {
+        criteria.baseline.target.extraNodal = {
+            // -
+            longestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: 20,
+                    message: '^Extranodal lesions must be >= %{count} mm on chest X-ray'
+                }
+            }
+        };
+    } else {
+        criteria.baseline.target.extraNodal = {
+            longestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: 10,
+                    message: '^Extranodal target lesions must be >= %{count} mm long axis'
+                }
+            }
+        };
+    }
+
+    return criteria;
+}
+
+/**
+ * irRC Trial Criteria Definition
+ * 
+ * Baseline Checks:
+ * - Target lesions must be >/= 10 X 10 mm
+ * - 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)
+ */
+function irRC(image) {
+    var acquisitionSliceThickness;
+    if (image) {
+        acquisitionSliceThickness = image.acquisitionSliceThickness;
+    }
+
+    // Define the irRC structure
+    var criteria = {
+        baseline: {
+            target: {},
+            nonTarget: {}
+        },
+        followup: {
+            newLesions: {
+                target: {}
+            },
+            target: {}
+        },
+        all: {}
+    };
+
+    if (acquisitionSliceThickness) {
+        criteria.baseline.target.all = {
+            longestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: Math.min(10, acquisitionSliceThickness),
+                    message: '^Target lesions must be >= 10 mm long axis AND >= double the acquisition slice thickness (' +
+                    acquisitionSliceThickness + ' mm) for CT and MR.'
+                }
+            },
+            shortestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: Math.min(10, acquisitionSliceThickness),
+                    message: '^Target lesions must be >= 10 mm short axis AND >= double the acquisition slice thickness (' +
+                    acquisitionSliceThickness + ' mm) for CT and MR.'
+                }
+            }
+        };
+    } else {
+        criteria.baseline.target.all = {
+            longestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: 10,
+                    message: '^Target lesions must be >= %{count} mm long axis.'
+                }
+            },
+            shortestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: 10,
+                    message: '^Target lesions must be >= %{count} mm short axis.'
+                }
+            }
+        };
+    }
+
+    criteria.baseline.target.all.response = {
+        exclusion: {
+            within: {
+                CR: 'Complete Response (CR)',
+                UN: 'Unknown (UN)',
+                NE: 'Non-evaluable (NE)',
+                EX: 'Excluded (EX)'
+            },
+            message: '^^Target lesions must have a length and cannot be marked as %{value} at baseline.'
+        }
+    };
+
+    criteria.baseline.nonTarget.all = {
+        response: {
+            // This is a workaround since Validating equality to something is not implemented yet
+            // https://github.com/ansman/validate.js/issues/79
+            presence: {
+                message: "^Non-target lesions can only be assessed as 'Present' at Baseline"
+            },
+            inclusion: {
+                within: ['Present'],
+                message: "^Non-target lesions can only be assessed as 'Present' at Baseline"
+            }
+        }
+    };
+
+    criteria.baseline.perOrgan = {
+        numberOfLesionsPerOrgan: {
+            numericality: {
+                lessThanOrEqualTo: 5,
+                //message: '^A maximum of %{count} target lesions per organ are allowed at Baseline.'
+            }
+        }
+    };
+
+    criteria.baseline.group = {
+        totalNumberOfLesions: {
+            numericality: {
+                lessThanOrEqualTo: 10,
+                //message: '^A maximum of %{count} target lesions total are allowed at Baseline.'
+            }
+        }
+    };
+
+    if (acquisitionSliceThickness) {
+        criteria.followup.newLesions.target.all = {
+            // - New target lesions must be >/= 5 X 5 mm AND >/= double the acquisition slice thickness by CT and MR
+            longestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: Math.min(5, 2 * acquisitionSliceThickness),
+                    message: '^New target lesions must be >= 5 mm long axis AND >= double the acquisition slice thickness (' +
+                    acquisitionSliceThickness + ' mm) for CT and MR.'
+                }
+            },
+            shortestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: Math.min(5, 2 * acquisitionSliceThickness),
+                    message: '^New target lesions must be >= 5 mm short axis AND >= double the acquisition slice thickness (' +
+                    acquisitionSliceThickness + ' mm) for CT and MR.'
+                }
+            }
+        };
+    } else {
+        criteria.followup.newLesions.target.all = {
+            // - New target lesions must be >/= 5 X 5 mm
+            longestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: 5,
+                    message: '^New target lesions must be >= %{count} mm long axis.'
+                }
+            },
+            shortestDiameter: {
+                numericality: {
+                    greaterThanOrEqualTo: 5,
+                    message: '^New target lesions must be >= %{count} mm short axis.'
+                }
+            }
+        };
+    }
+
+    criteria.followup.group = {
+        numberOfLesionsPerOrgan: {
+            numericality: {
+                lessThanOrEqualTo: 5,
+                message: '^A maximum of %{count} target lesions per organ are allowed at Followup.'
+            }
+        },
+        totalNumberOfLesions: {
+            numericality: {
+                lessThanOrEqualTo: 10,
+                message: '^A maximum of %{count} target lesions total are allowed at Followup.'
+            }
+        }
+    };
+
+    // TODO: Check the actual requirement for total burden!
+    criteria.all.group = {
+        totalLesionBurden: {
+            numericality: {
+                greaterThanOrEqualTo: 100,
+                message: '^Total lesion burden (SPD target lesions + SPD new lesions) should be greater than %{count}.'
+            }
+        }
+    };
+
+    return criteria;
+}
+
+/**
+ * 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 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;
+    }
+
+    // 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);
+
+    // 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;
+    }
+
+    // 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
+    });
+
+    if (!study) {
+        log.warn('No study/timepoint association.');
+        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];
+};

Packages/lesiontracker/lib/TrialResponseCriteria.js

@@ -0,0 +1,343 @@
+// Create a client-only Collection to store our Validation Errors
+ValidationErrors = new Meteor.Collection(null);
+
+// Set Validate.js Library's default options
+validate.options = {
+    format: 'detailed'
+};
+
+/**
+ * Creates an array of validation error messages given an Object of validation errors
+ * and an optional prefix for the messages. An example of a useful prefix would be
+ * the location of the measurement or something like 'Target 1 '.
+ *
+ * @param validationErrors
+ * @param prefix
+ */
+function addValidationErrorsToCollection(validationErrors, prefix, type) {
+    // If no input was given, stop here
+    if (!validationErrors || !validationErrors.length) {
+        return;
+    }
+
+    // Loop through each of the entries in the validationErrors Array
+    validationErrors.forEach(function(validationError) {
+        var existingError = ValidationErrors.findOne({
+            attribute: validationError.attribute,
+            validator: validationError.validator,
+            error: validationError.error,
+            prefix: prefix
+        });
+
+        if (existingError) {
+            ValidationErrors.update(existingError._id, {
+                $set: {
+                    value: validationError.value
+                }
+            });
+        } else {
+            validationError.type = type;
+            validationError.prefix = prefix;
+            ValidationErrors.insert(validationError);
+        }
+    });
+}
+
+/**
+ * Runs conformance checks related to a group of measurements. This function
+ * searches the input object of Constraints and looks for the 'group' attribute.
+ *
+ * It calculates some general group-level values for the current set of Measurements
+ * and validates these using the input constraints.
+ *
+ * @param constraints
+ * @returns {Array} Array of error messages related to the input conformance checks
+ */
+function assessGroupOfMeasurements(constraints) {
+    // Retrieve the group-level constraints
+    var groupConstraints = constraints.group;
+
+    // If no group-level constraints exist, stop here
+    if (!groupConstraints) {
+        return;
+    }
+
+    var type = 'group';
+    ValidationErrors.remove({
+        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)
+    };
+
+    // Run the conformance checks with the validate.js library
+    var validationErrors = validate(testStructure, groupConstraints);
+
+    // Return any error messages as a flattened array of errors
+    addValidationErrorsToCollection(validationErrors, '', type);
+}
+
+/**
+ * Runs conformance checks related to per-organ sets of measurements.
+ *
+ * This function searches the input object of Constraints and looks for the
+ * 'perOrgan' attribute.
+ *
+ * It calculates some general per-organ statistics for the current set of Measurements
+ * and validates these using the input constraints.
+ *
+ * @param constraints
+ * @returns {Array} Array of error messages related to the input conformance checks
+ */
+function assessMeasurementPerOrgan(constraints) {
+    // Retrieve the per-organ constraints
+    var perOrganConstraints = constraints.perOrgan;
+
+    // If no per-organ constraints exist, stop here
+    if (!perOrganConstraints) {
+        return;
+    }
+
+    // Create a list of all unique locations that contain measurements
+    // by looping through the Measurements Collection
+    var organLocations = [];
+    Measurements.find().forEach(function(measurement) {
+        if (organLocations.indexOf(measurement.location) > -1) {
+            return;
+        }
+
+        organLocations.push(measurement.location);
+    });
+
+    var type = 'perOrgan';
+    ValidationErrors.remove({
+        type: type
+    });
+
+    // Loop through each unique organ location in order to validate
+    // the per-organ constraints for each organ
+    organLocations.forEach(function(location) {
+        // Calculate the number of Lesions per Organ
+        var numberOfLesionsPerOrgan = Measurements.find({
+            location: location
+        }).count();
+
+        // Store per-organ Measurement statistics for validation
+        // Right now this is only the numberOfLesionsPerOrgan, but later
+        // this may include other checks
+        var testStructure = {
+            numberOfLesionsPerOrgan: numberOfLesionsPerOrgan
+        };
+
+        // Run the conformance checks with the validate.js library
+        var validationErrors = validate(testStructure, perOrganConstraints);
+
+        // Obtain any error messages as a flattened array of errors, prefixed
+        // with the Organ name, in the form 'Liver Left: '
+        addValidationErrorsToCollection(validationErrors, location + ': ', type);
+    });
+}
+
+/**
+ * Runs conformance checks on a single Measurement given the
+ * cornerstone toolData related to it.
+ *
+ * @param constraints
+ * @param measurementData CornerstoneTools toolData Object for this specific Measurement
+ * @returns {Array} Array of error messages related to the input conformance checks
+ */
+function assessSingleMeasurement(constraints, measurementData) {
+    // Check whether this is a Target or Non-Target Measurement
+    var targetType = measurementData.isTarget ? 'target' : 'nonTarget';
+
+    // Retrieve any target/non-target-specific single-measurement constraints
+    // from the input constraint structure
+    var measurementConstraints = constraints[targetType];
+
+    // If no relevant constraints exist, stop here
+    if (!measurementConstraints) {
+        return;
+    }
+
+    // Check whether this is a Nodal or Extranodal Measurement
+    var nodalType = measurementData.isNodal ? 'nodal' : 'extraNodal';
+
+    // Retrieve any nodal/extra-nodal-specific constraints to see if we can apply them
+    var constraintsToApply;
+    if (measurementData.isNodal !== undefined && measurementConstraints[nodalType]) {
+        // Check if we have enough information (about nodality of this Measurement,
+        // and nodality-specific constraints) to apply nodality-specific constraints
+        constraintsToApply = measurementConstraints[nodalType];
+    } else if (measurementConstraints.all) {
+        // If we have no data about the nodality of this Measurement, or no relevant
+        // specific constraints, we should apply the constraints valid for 'all' nodality
+        // types
+        constraintsToApply = measurementConstraints.all;
+    }
+
+    // Calculate a lesion name based on whether or not we have a Target or Non-target
+    // Measurement, and the lesion number of this Measurement.
+    var lesionName = measurementData.isTarget ? 'Target' : 'Non-target';
+    lesionName = lesionName + ' ' + measurementData.lesionNumber + ': ';
+
+    ValidationErrors.remove({
+        prefix: lesionName
+    });
+
+    // Use validate.js to check the criteria
+    var validationErrors = validate(measurementData, constraintsToApply);
+
+    if (validationErrors) {
+        validationErrors.forEach(function(error) {
+            error.measurementId = measurementData._id;
+        });
+    }
+
+    // Use the Lesion Name as a prefix to concatenate any validation error messages into
+    // an array to return
+    addValidationErrorsToCollection(validationErrors, lesionName);
+}
+
+/**
+ * Validate from a single Measurement up the chain to include group and perOrgan
+ * conformance checks
+ *
+ * @param measurementData The CornerstoneTools toolData for a single Measurement
+ */
+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);
+
+    if (!currentConstraints) {
+        log.warn('No relevant contraints could be applied');
+        return;
+    }
+
+    // Find the relevant Measurement in the Measurements Collection
+    var measurement = Measurements.findOne(measurementData.id);
+
+    // If no such Measurement exists, stop here
+    if (!measurement) {
+        log.warn('No Measurement found?');
+        return;
+    }
+
+    // Find the current timepointId that the user was editing the Measurement on
+    var timepointId = measurementData.timepointId;
+
+    // Find the specific measurement data for this Measurement at this Timepoint
+    var currentMeasurement = measurement.timepoints[timepointId];
+
+    // Include target and nodal flags on the timepoint-specific data so it is easier to validate
+    // TODO: Rethink what to pass to assessSingleMeasurement?
+    currentMeasurement.isTarget = measurement.isTarget;
+    currentMeasurement.isNodal = measurement.isNodal;
+    currentMeasurement.lesionNumber = measurement.lesionNumber;
+    currentMeasurement._id = measurement._id;
+
+    // Run the single-measurement-specific conformance checks
+    // If any messages exist, add them to the array of messages
+    assessSingleMeasurement(currentConstraints, currentMeasurement);
+
+    validateGroups();
+}
+
+function validateGroups() {
+    // Obtain the name of the current TrialResponseAssessmentCriteria that
+    // we are using.
+    var criteriaType = Session.get('TrialResponseAssessmentCriteria');
+
+    Timepoints.find().forEach(function(timepoint) {
+        // TODO: Criteria for the specific image are retrieved from the general set of criteria.
+        // - The acquisitionSliceThickness, for example, may be pulled from the image metadata
+        // - The organ in question, e.g. Chest X-ray, may determine the exact specifications for the current trial criteria
+        var currentConstraints = getTrialCriteriaConstraints(criteriaType);
+
+        // Retrieve the current constraints which apply to the specific Timepoint type
+        // (e.g. baseline, followup) that this Measurement is being edited on.
+        var timepointConstraints = currentConstraints[timepoint.timepointType];
+        if (!timepointConstraints) {
+            return;
+        }
+
+        // Run the group-level conformance checks
+        assessGroupOfMeasurements(timepointConstraints);
+
+        // Run the per-organ conformance checks
+        assessMeasurementPerOrgan(timepointConstraints);
+    });
+}
+
+function validateAll() {
+    // Obtain the name of the current TrialResponseAssessmentCriteria that
+    // we are using.
+    var criteriaType = Session.get('TrialResponseAssessmentCriteria');
+
+    Measurements.find().forEach(function(measurement) {
+        Object.keys(measurement.timepoints).forEach(function(timepointId) {
+            var currentMeasurement = measurement.timepoints[timepointId];
+            currentMeasurement.isTarget = measurement.isTarget;
+            currentMeasurement.isNodal = measurement.isNodal;
+            currentMeasurement.lesionNumber = measurement.lesionNumber;
+            currentMeasurement._id = measurement._id;
+
+            // TODO: Criteria for the specific image are retrieved from the general set of criteria.
+            // - The acquisitionSliceThickness, for example, may be pulled from the image metadata
+            // - The organ in question, e.g. Chest X-ray, may determine the exact specifications for the current trial criteria
+            var currentConstraints = getTrialCriteriaConstraints(criteriaType, currentMeasurement.imageId);
+
+            // Run the single-measurement-specific conformance checks
+            // If any messages exist, add them to the array of messages
+            assessSingleMeasurement(currentConstraints, currentMeasurement);
+        });
+    });
+    validateGroups();
+}
+
+var validationTimeout = 400;
+
+/**
+ * Validate the measurements after a set delay period
+ *
+ * @param measurementData Input measurement data from CornerstoneTools
+ */
+function validateDelayed(measurementData) {
+    // Erase any currently-waiting validation call
+    clearTimeout(validationTimeout);
+
+    // Set a timeout to run validation after a delay
+    // Currently this is 400 milliseconds
+    setTimeout(function() {
+        validateSingleMeasurement(measurementData);
+    }, validationTimeout);
+}
+
+/**
+ * Validate all measurements after a set delay period
+ */
+function validateAllDelayed() {
+    // Erase any currently-waiting validation call
+    clearTimeout(validationTimeout);
+
+    // Set a timeout to run validation after a delay
+    // Currently this is 400 milliseconds
+    setTimeout(function() {
+        validateAll();
+    }, validationTimeout);
+}
+
+TrialResponseCriteria = {
+    validateAll: validateAll,
+    validateAllDelayed: validateAllDelayed,
+    validateSingleMeasurement: validateSingleMeasurement,
+    validateDelayed: validateDelayed,
+    validateGroups: validateGroups
+};

Packages/lesiontracker/lib/activateMeasurements.js

@@ -12,7 +12,7 @@ activateMeasurements = function(element, measurementId, templateData, viewportIn
     var timepointData = getTimepointObject(imageId);
     var measurementData = Measurements.findOne(measurementId);
 
-    var measurementAtTimepoint = measurementData.timepoints[timepointData.timepointID];
+    var measurementAtTimepoint = measurementData.timepoints[timepointData.timepointId];
     if (!measurementAtTimepoint) {
         return;
     }
@@ -35,11 +35,11 @@ activateMeasurements = function(element, measurementId, templateData, viewportIn
     }
 
     if (imageIdIndex === elementCurrentImageIdIndex) {
-        activateTool(element, measurementData, timepointData.timepointID);
+        activateTool(element, measurementData, timepointData.timepointId);
     } else {
         cornerstone.loadAndCacheImage(imageIds[imageIdIndex]).then(function(image) {
             cornerstone.displayImage(element, image);
-            activateTool(element, measurementData, timepointData.timepointID);
+            activateTool(element, measurementData, timepointData.timepointId);
         });
     }
 };
@@ -50,9 +50,9 @@ activateMeasurements = function(element, measurementId, templateData, viewportIn
  *
  * @param element
  * @param measurementData
- * @param timepointID
+ * @param timepointId
  */
-function activateTool(element, measurementData, timepointID) {
+function activateTool(element, measurementData, timepointId) {
     deactivateAllToolData(element, 'lesion');
     deactivateAllToolData(element, 'nonTarget');
 
@@ -62,7 +62,7 @@ function activateTool(element, measurementData, timepointID) {
         return;
     }
 
-    var measurementAtTimepoint = measurementData.timepoints[timepointID];
+    var measurementAtTimepoint = measurementData.timepoints[timepointId];
 
     for (var i = 0; i < toolData.data.length; i++) {
         data = toolData.data[i];

Packages/lesiontracker/lib/calculateTotalLesionBurden.js

@@ -0,0 +1,59 @@
+/**
+ * Calculates total lesion burden given the Trial Criteria Type.
+ * Supports RECIST 1.1 and irRC at present, defaults to RECIST.
+ *
+ * @param criteriaType Either 'RECIST' or 'irRC'
+ * @returns {*}
+ */
+calculateTotalLesionBurden = function(criteriaType) {
+    var totalBurden;
+    var measurements = Measurements.find({
+        isTarget: true
+    });
+
+    switch (criteriaType) {
+        default:
+        case 'RECIST':
+            // - Time Point Measurement Total =
+            // Sum of long axis measurements for extranodal target lesion +
+            //        short axis measurements for nodal lesions
+            var sumLongAxisExtranodal = 0,
+                sumShortAxisNodal = 0;
+
+            measurements.forEach(function(measurement) {
+                var LD = parseFloat(measurement.longestDiameter);
+                var SD = parseFloat(measurement.longestDiameter);
+
+                if (measurement.nodal === true) {
+                    sumShortAxisNodal += SD;
+                } else {
+                    sumLongAxisExtranodal += LD;
+                }
+            });
+
+            totalBurden = sumLongAxisExtranodal + sumShortAxisNodal;
+            break;
+        case 'irRC':
+            // - Time Point Measurement Total = SPD target lesions + SPD new lesions
+            // (SPD = sum of product of long axis and short axis diameters)
+            var sumProductLesions = 0,
+                sumProductNewLesions = 0;
+
+            measurements.forEach(function(measurement) {
+                var LD = parseFloat(measurement.longestDiameter);
+                var SD = parseFloat(measurement.shortestDiameter);
+                var product = LD * SD;
+
+                if (measurement.newLesion === true) {
+                    sumProductNewLesions += product;
+                } else {
+                    sumProductLesions += product;
+                }
+            });
+
+            totalBurden = sumProductLesions + sumProductNewLesions;
+            break;
+    }
+
+    return totalBurden;
+};

Packages/lesiontracker/lib/clearMeasurementTimepointData.js

@@ -19,12 +19,11 @@ clearMeasurementTimepointData = function(measurementId, timepointId) {
 
     delete data.timepoints[timepointId];
 
-    if (Object.keys(data.timepoints).length === 0) {
+    if (!Object.keys(data.timepoints).length) {
         Meteor.call('removeMeasurement', measurementId, function(error, response) {
             if (error) {
                 log.warn(error);
             }
-            console.log('Removed!');
         });
     } else {
         // Update the Timepoint object of the Measurement document

Packages/lesiontracker/lib/clearTools.js

@@ -35,4 +35,7 @@ clearTools = function() {
 
     // Remove patient's measurements
     Meteor.call('removeMeasurementsByPatientId', patientId);
+
+    // Clear all validation errors
+    ValidationErrors.remove({});
 };

Packages/lesiontracker/lib/getTimepointName.js

@@ -0,0 +1,44 @@
+/**
+ * Calculates a Timepoint's name based on how many timepoints exist between it
+ * and the latest Baseline. Names returned are in the form of 'Baseline', or
+ * 'Follow-up 1', 'Follow-up 2', and so on.
+ *
+ * @param timepoint
+ * @returns {*} The timepoint name
+ */
+getTimepointName = function(timepoint) {
+    // Check if this is a Baseline timepoint, if it is, return 'Baseline'
+    if (timepoint.timepointType === 'baseline') {
+        return 'Baseline';
+    }
+
+    // Retrieve all of the relevant follow-up timepoints for this patient
+    var followupTimepoints = Timepoints.find({
+        patientId: timepoint.patientId,
+        timepointType: timepoint.timepointType
+    }, {
+        sort: {
+            latestDate: 1
+        }
+    });
+
+    // Create an array of just timepointIds, so we can use indexOf
+    // on it to find the current timepoint's relative position
+    var followupTimepointIds = followupTimepoints.map(function(timepoint) {
+        return timepoint.timepointId;
+    });
+
+    // Calculate the index of the current timepoint in the array of all
+    // relevant follow-up timepoints
+    var index = followupTimepointIds.indexOf(timepoint.timepointId) + 1;
+
+    // If index is 0, it means that the current timepoint was not in the list
+    // Log a warning and return here
+    if (!index) {
+        log.warn('Current follow-up was not in the list of relevant follow-ups?');
+        return;
+    }
+
+    // Return the timepoint name as 'Follow-up N'
+    return 'Follow-up ' + index;
+};

Packages/lesiontracker/lib/getTimepointObject.js

@@ -11,6 +11,8 @@ getTimepointObject = function(imageId) {
     }
 
     return Timepoints.findOne({
-        timepointName: study.studyDate
+        studyInstanceUids: {
+            $in: [study.studyInstanceUid]
+        }
     });
 };

Packages/lesiontracker/lib/handleMeasurementAdded.js

@@ -0,0 +1,12 @@
+handleMeasurementAdded = function(e, eventData) {
+    log.info('CornerstoneToolsMeasurementAdded');
+    var measurementData = eventData.measurementData;
+
+    switch (eventData.toolType) {
+        case 'nonTarget':
+        case 'lesion':
+            LesionManager.updateLesionData(measurementData);
+            TrialResponseCriteria.validateDelayed(measurementData);
+            break;
+    }
+};

Packages/lesiontracker/lib/handleMeasurementModified.js

@@ -0,0 +1,12 @@
+handleMeasurementModified = function(e, eventData) {
+    log.info('CornerstoneToolsMeasurementModified');
+    var measurementData = eventData.measurementData;
+
+    switch (eventData.toolType) {
+        case 'nonTarget':
+        case 'lesion':
+            LesionManager.updateLesionData(measurementData);
+            TrialResponseCriteria.validateDelayed(measurementData);
+            break;
+    }
+};

Packages/lesiontracker/lib/handleMeasurementRemoved.js

@@ -0,0 +1,19 @@
+handleMeasurementRemoved = function(e, eventData) {
+    log.info('CornerstoneToolsMeasurementRemoved');
+    var measurementData = eventData.measurementData;
+
+    switch (eventData.toolType) {
+        case 'nonTarget':
+        case 'lesion':
+            var measurement = Measurements.findOne(measurementData.id, {
+                reactive: false
+            });
+
+            if (!measurement) {
+                return;
+            }
+
+            clearMeasurementTimepointData(measurement._id, measurementData.timepointId);
+            break;
+    }
+};

Packages/lesiontracker/lib/pixelSpacingAutorunCheck.js

@@ -0,0 +1,30 @@
+pixelSpacingAutorunCheck = function() {
+    log.info('lesionTool button change autorun');
+    /*if (!Session.get('ViewerData')) {
+        return;
+    }*/
+
+    // Get oncology tools
+    var oncologyTools = $('button#lesion, button#nonTarget');
+
+    // TODO: Set activeViewport for empty viewport element
+    var activeViewportIndex = Session.get('activeViewport');
+    if (activeViewportIndex === undefined) {
+        return;
+    }
+
+    var element = $('.imageViewerViewport').get(activeViewportIndex);
+    var enabledElement = cornerstone.getEnabledElement(element);
+
+    // Check value of rowPixelSpacing & columnPixelSpacing to define as unavailable
+    if (!enabledElement ||
+        !enabledElement.image ||
+        !enabledElement.image.rowPixelSpacing ||
+        !enabledElement.image.columnPixelSpacing) {
+        // Disable Lesion Buttons
+        oncologyTools.prop('disabled', true);
+    } else {
+        // Enable Lesion Buttons
+        oncologyTools.prop('disabled', false);
+    }
+};

Packages/lesiontracker/lib/syncMeasurementAndToolData.js

@@ -0,0 +1,75 @@
+syncMeasurementAndToolData = function(data) {
+    // Check what toolType we should be adding this to, based on the isTarget value
+    // of the stored Measurement
+    var toolType = data.isTarget ? 'lesion' : 'nonTarget';
+    var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
+
+    // Loop through the timepoint data for this measurement
+    Object.keys(data.timepoints).forEach(function(key) {
+        var storedData = data.timepoints[key];
+        var imageId = storedData.imageId;
+
+        if (!toolState[imageId]) {
+            toolState[imageId] = {};
+        }
+
+        // This is probably not the best approach to prevent duplicates
+        if (toolState[imageId][toolType] && toolState[imageId][toolType].data) {
+            var measurementHasNoIdYet = false;
+            toolState[imageId][toolType].data.forEach(function(measurement) {
+                if (measurement.id === 'notready') {
+                    measurementHasNoIdYet = true;
+                    return false;
+                }
+            });
+
+            // Stop here if it appears that we are creating this measurement right now,
+            // and would not like this function to add another copy of it to the toolData
+            if (measurementHasNoIdYet === true) {
+                return;
+            }
+        }
+
+        if (!toolState[imageId][toolType]) {
+            toolState[imageId][toolType] = {
+                data: []
+            };
+        } else {
+            var alreadyExists = false;
+            if (toolState[imageId][toolType].data.length) {
+                toolState[imageId][toolType].data.forEach(function(measurement) {
+                    if (measurement.id === data._id) {
+                        alreadyExists = true;
+
+                        // Update the toolData lesionNumber from the Measurement
+                        measurement.lesionNumber = data.lesionNumber;
+                        return false;
+                    }
+                });
+            }
+
+            if (alreadyExists === true) {
+                return;
+            }
+        }
+
+        // Create measurementData structure based on the lesion data at this timepoint
+        // We will add this into the toolData for this imageId
+        var measurementData = storedData;
+        measurementData.isTarget = data.isTarget;
+        measurementData.lesionNumber = data.lesionNumber;
+        measurementData.measurementText = data.measurementText;
+        measurementData.isDeleted = data.isDeleted;
+        measurementData.location = data.location;
+        measurementData.locationUID = data.locationUID;
+        measurementData.patientId = patientId;
+        measurementData.visible = data.visible;
+        measurementData.active = data.active;
+        measurementData.uid = data.uid;
+        measurementData.id = data._id;
+
+        toolState[imageId][toolType].data.push(measurementData);
+
+        TrialResponseCriteria.validateSingleMeasurement(measurementData);
+    });
+};

Packages/lesiontracker/lib/updateRelatedElements.js

@@ -0,0 +1,13 @@
+updateRelatedElements = function(imageId) {
+    // Get all on-screen elements with this imageId
+    var enabledElements = cornerstone.getEnabledElementsByImageId(imageId);
+
+    // TODO=Check original event to prevent duplicate updateImage calls
+
+    // Loop through these elements
+    enabledElements.forEach(function(enabledElement) {
+        // Update the display so the tool is removed
+        var element = enabledElement.element;
+        cornerstone.updateImage(element);
+    });
+};

Packages/lesiontracker/lib/uuid.js

@@ -1,250 +0,0 @@
-//     uuid.js
-//
-//     Copyright (c) 2010-2012 Robert Kieffer
-//     MIT License - http://opensource.org/licenses/mit-license.php
-
-(function() {
-    var _global = this;
-
-    // Unique ID creation requires a high quality random # generator.  We feature
-    // detect to determine the best RNG source, normalizing to a function that
-    // returns 128-bits of randomness, since that's what's usually required
-    var _rng;
-
-    // Allow for MSIE11 msCrypto
-    var _crypto = _global.crypto || _global.msCrypto;
-
-    // Node.js crypto-based RNG - http://nodejs.org/docs/v0.6.2/api/crypto.html
-    //
-    // Moderately fast, high quality
-    if (typeof(_global.require) == 'function') {
-        try {
-            var _rb = _global.require('crypto').randomBytes;
-            _rng = _rb && function() {return _rb(16);};
-        } catch(e) {}
-    }
-
-    if (!_rng && _crypto && _crypto.getRandomValues) {
-        // WHATWG crypto-based RNG - http://wiki.whatwg.org/wiki/Crypto
-        //
-        // Moderately fast, high quality
-        var _rnds8 = new Uint8Array(16);
-        _rng = function whatwgRNG() {
-            _crypto.getRandomValues(_rnds8);
-            return _rnds8;
-        };
-    }
-
-    if (!_rng) {
-        // Math.random()-based (RNG)
-        //
-        // If all else fails, use Math.random().  It's fast, but is of unspecified
-        // quality.
-        var _rnds = new Array(16);
-        _rng = function() {
-            for (var i = 0, r; i < 16; i++) {
-                if ((i & 0x03) === 0) r = Math.random() * 0x100000000;
-                _rnds[i] = r >>> ((i & 0x03) << 3) & 0xff;
-            }
-
-            return _rnds;
-        };
-    }
-
-    // Buffer class to use
-    var BufferClass = typeof(_global.Buffer) == 'function' ? _global.Buffer : Array;
-
-    // Maps for number <-> hex string conversion
-    var _byteToHex = [];
-    var _hexToByte = {};
-    for (var i = 0; i < 256; i++) {
-        _byteToHex[i] = (i + 0x100).toString(16).substr(1);
-        _hexToByte[_byteToHex[i]] = i;
-    }
-
-    // **`parse()` - Parse a UUID into it's component bytes**
-    function parse(s, buf, offset) {
-        var i = (buf && offset) || 0, ii = 0;
-
-        buf = buf || [];
-        s.toLowerCase().replace(/[0-9a-f]{2}/g, function(oct) {
-            if (ii < 16) { // Don't overflow!
-                buf[i + ii++] = _hexToByte[oct];
-            }
-        });
-
-        // Zero out remaining bytes if string was short
-        while (ii < 16) {
-            buf[i + ii++] = 0;
-        }
-
-        return buf;
-    }
-
-    // **`unparse()` - Convert UUID byte array (ala parse()) into a string**
-    function unparse(buf, offset) {
-        var i = offset || 0, bth = _byteToHex;
-        return bth[buf[i++]] + bth[buf[i++]] +
-                bth[buf[i++]] + bth[buf[i++]] + '-' +
-                bth[buf[i++]] + bth[buf[i++]] + '-' +
-                bth[buf[i++]] + bth[buf[i++]] + '-' +
-                bth[buf[i++]] + bth[buf[i++]] + '-' +
-                bth[buf[i++]] + bth[buf[i++]] +
-                bth[buf[i++]] + bth[buf[i++]] +
-                bth[buf[i++]] + bth[buf[i++]];
-    }
-
-    // **`v1()` - Generate time-based UUID**
-    //
-    // Inspired by https://github.com/LiosK/UUID.js
-    // and http://docs.python.org/library/uuid.html
-
-    // random #'s we need to init node and clockseq
-    var _seedBytes = _rng();
-
-    // Per 4.5, create and 48-bit node id, (47 random bits + multicast bit = 1)
-    var _nodeId = [
-      _seedBytes[0] | 0x01,
-      _seedBytes[1], _seedBytes[2], _seedBytes[3], _seedBytes[4], _seedBytes[5]
-    ];
-
-    // Per 4.2.2, randomize (14 bit) clockseq
-    var _clockseq = (_seedBytes[6] << 8 | _seedBytes[7]) & 0x3fff;
-
-    // Previous uuid creation time
-    var _lastMSecs = 0, _lastNSecs = 0;
-
-    // See https://github.com/broofa/node-uuid for API details
-    function v1(options, buf, offset) {
-        var i = buf && offset || 0;
-        var b = buf || [];
-
-        options = options || {};
-
-        var clockseq = options.clockseq != null ? options.clockseq : _clockseq;
-
-        // UUID timestamps are 100 nano-second units since the Gregorian epoch,
-        // (1582-10-15 00:00).  JSNumbers aren't precise enough for this, so
-        // time is handled internally as 'msecs' (integer milliseconds) and 'nsecs'
-        // (100-nanoseconds offset from msecs) since unix epoch, 1970-01-01 00:00.
-        var msecs = options.msecs != null ? options.msecs : new Date().getTime();
-
-        // Per 4.2.1.2, use count of uuid's generated during the current clock
-        // cycle to simulate higher resolution clock
-        var nsecs = options.nsecs != null ? options.nsecs : _lastNSecs + 1;
-
-        // Time since last uuid creation (in msecs)
-        var dt = (msecs - _lastMSecs) + (nsecs - _lastNSecs) / 10000;
-
-        // Per 4.2.1.2, Bump clockseq on clock regression
-        if (dt < 0 && options.clockseq == null) {
-            clockseq = clockseq + 1 & 0x3fff;
-        }
-
-        // Reset nsecs if clock regresses (new clockseq) or we've moved onto a new
-        // time interval
-        if ((dt < 0 || msecs > _lastMSecs) && options.nsecs == null) {
-            nsecs = 0;
-        }
-
-        // Per 4.2.1.2 Throw error if too many uuids are requested
-        if (nsecs >= 10000) {
-            throw new Error('uuid.v1(): Can\'t create more than 10M uuids/sec');
-        }
-
-        _lastMSecs = msecs;
-        _lastNSecs = nsecs;
-        _clockseq = clockseq;
-
-        // Per 4.1.4 - Convert from unix epoch to Gregorian epoch
-        msecs += 12219292800000;
-
-        // `time_low`
-        var tl = ((msecs & 0xfffffff) * 10000 + nsecs) % 0x100000000;
-        b[i++] = tl >>> 24 & 0xff;
-        b[i++] = tl >>> 16 & 0xff;
-        b[i++] = tl >>> 8 & 0xff;
-        b[i++] = tl & 0xff;
-
-        // `time_mid`
-        var tmh = (msecs / 0x100000000 * 10000) & 0xfffffff;
-        b[i++] = tmh >>> 8 & 0xff;
-        b[i++] = tmh & 0xff;
-
-        // `time_high_and_version`
-        b[i++] = tmh >>> 24 & 0xf | 0x10; // include version
-        b[i++] = tmh >>> 16 & 0xff;
-
-        // `clock_seq_hi_and_reserved` (Per 4.2.2 - include variant)
-        b[i++] = clockseq >>> 8 | 0x80;
-
-        // `clock_seq_low`
-        b[i++] = clockseq & 0xff;
-
-        // `node`
-        var node = options.node || _nodeId;
-        for (var n = 0; n < 6; n++) {
-            b[i + n] = node[n];
-        }
-
-        return buf ? buf : unparse(b);
-    }
-
-    // **`v4()` - Generate random UUID**
-
-    // See https://github.com/broofa/node-uuid for API details
-    function v4(options, buf, offset) {
-        // Deprecated - 'format' argument, as supported in v1.2
-        var i = buf && offset || 0;
-
-        if (typeof(options) == 'string') {
-            buf = options == 'binary' ? new BufferClass(16) : null;
-            options = null;
-        }
-
-        options = options || {};
-
-        var rnds = options.random || (options.rng || _rng)();
-
-        // Per 4.4, set bits for version and `clock_seq_hi_and_reserved`
-        rnds[6] = (rnds[6] & 0x0f) | 0x40;
-        rnds[8] = (rnds[8] & 0x3f) | 0x80;
-
-        // Copy bytes to buffer, if provided
-        if (buf) {
-            for (var ii = 0; ii < 16; ii++) {
-                buf[i + ii] = rnds[ii];
-            }
-        }
-
-        return buf || unparse(rnds);
-    }
-
-    // Export public API
-    var uuid = v4;
-    uuid.v1 = v1;
-    uuid.v4 = v4;
-    uuid.parse = parse;
-    uuid.unparse = unparse;
-    uuid.BufferClass = BufferClass;
-
-    if (typeof(module) != 'undefined' && module.exports) {
-        // Publish as node.js module
-        module.exports = uuid;
-    } else if (typeof define === 'function' && define.amd) {
-        // Publish as AMD module
-        define(function() {return uuid;});
- 
-    } else {
-        // Publish as global (in browsers)
-        var _previousRoot = _global.uuid;
-
-        // **`noConflict()` - (browser only) to reset global 'uuid' var**
-        uuid.noConflict = function() {
-            _global.uuid = _previousRoot;
-            return uuid;
-        };
-
-        _global.uuid = uuid;
-    }
-}).call(this);

Packages/lesiontracker/lib/worklist/openNewTabWithTimepoint.js

@@ -0,0 +1,108 @@
+/**
+ * Opens a new tab in the tabbed worklist environment using
+ * a given timepoint and new tab title.
+ *
+ * @param timepointId The UID of the Timepoint to be opened
+ * @param title The title to be used for the tab heading
+ */
+openNewTabWithTimepoint = function(timepointId, title) {
+    log.info('openNewTabWithTimepoint: ' + timepointId + ' ' + title);
+
+    // Generate a unique ID to represent this tab
+    // We can't just use the Mongo entry ID because
+    // then it will change after hot-reloading.
+    var contentid = uuid.new();
+
+    var timepoint = Timepoints.findOne({
+        timepointId: timepointId
+    });
+    
+    if (!timepoint) {
+        throw 'No such timepoint exists';
+    }
+
+    // Get the relevant studyInstanceUids given the timepoints
+    var data = getDataFromTimepoint(timepoint);
+    if (!data.studyInstanceUids) {
+        throw 'No studies found that are related to this timepoint';
+    }
+
+    // Create a new entry in the WorklistTabs Collection
+    WorklistTabs.insert({
+        title: title,
+        contentid: contentid,
+        active: false,
+        timepointId: timepointId
+    });
+
+    // Update the ViewerData global object
+    ViewerData[contentid] = {
+        title: title,
+        contentid: contentid,
+        studyInstanceUids: data.studyInstanceUids,
+        timepointIds: data.timepointIds
+    };
+
+    // Switch to the new tab
+    switchToTab(contentid);
+};
+
+/**
+ * Retrieves related studies given a Baseline or Follow-up Timepoint
+ *
+ * @param timepoint
+ * @returns {Array}
+ */
+function getDataFromTimepoint(timepoint) {
+    var relatedStudies = [];
+
+    // Include the specified studyInstanceUids
+    // NOTE: Temporarily added [0], since we only need one study per timepoint to load immediately?
+    relatedStudies = relatedStudies.concat(timepoint.studyInstanceUids[0]);
+
+    // If this is the baseline, we should stop here and return the relevant studies
+    if (isBaseline(timepoint)) {
+        return {
+            studyInstanceUids: relatedStudies,
+            timepointIds: [timepoint.timepointId]
+        };
+    }
+
+    // Otherwise, this is a follow-up exam, so we should also find the baseline timepoint,
+    // and all studies related to it. We also enforce that the Baseline should have a studyDate
+    // prior to the latest studyDate in the current (Follow-up) Timepoint.
+    var baseline = Timepoints.findOne({
+        timepointType: 'baseline',
+        patientId: timepoint.patientId,
+        latestDate: {
+            $lte: timepoint.latestDate
+        }
+    });
+
+    var timepointIds = [];
+    if (baseline) {
+        // NOTE: Temporarily added [0], since we only need one study per timepoint to load immediately?
+        relatedStudies = relatedStudies.concat(baseline.studyInstanceUids[0]);
+        timepointIds.push(baseline.timepointId);
+    } else {
+        log.warn('No Baseline found while opening a Follow-up Timepoint');
+    }
+
+    timepointIds.push(timepoint.timepointId);
+
+    return {
+        studyInstanceUids: relatedStudies,
+        timepointIds: timepointIds
+    };
+}
+
+/**
+ * Checks if a Timepoints is a baseline or not
+ * (abstracting this for later use, since I expect it to get more complex)
+ *
+ * @param timepoint a document from the Timepoints Collection
+ * @returns {boolean} Whether or not the timepoint is stored as a Baseline
+ */
+function isBaseline(timepoint) {
+    return (timepoint.timepointType === 'baseline');
+}

Packages/lesiontracker/lib/worklist/worklistModification.js

@@ -0,0 +1,37 @@
+Meteor.startup(function() {
+    Worklist.subscriptions = ['studies', 'timepoints'];
+    Worklist.callbacks['dblClickOnStudy'] = dblClickOnStudy;
+    Worklist.callbacks['middleClickOnStudy'] = dblClickOnStudy;
+});
+
+/**
+ * Lesion Tracker method including Timepoints / other studies
+ */
+function dblClickOnStudy(data) {
+    // Use the formatPN template helper to clean up the patient name
+    var title = formatPN(data.patientName);
+    var study = Studies.findOne({
+        studyInstanceUid: data.studyInstanceUid
+    });
+
+    // Check if the study has been associated, and if not, just open it on its own
+    if (!study) {
+        // Open a new tab with this study
+        openNewTab(data.studyInstanceUid, title);
+        return;
+    }
+
+    // Find the relevant timepoint given the clicked-on study
+    var timepoint = Timepoints.findOne({
+        studyInstanceUids: {
+            $in: [data.studyInstanceUid]
+        }
+    });
+
+    if (!timepoint) {
+        openNewTab(data.studyInstanceUid, title);
+        return;
+    }
+
+    openNewTabWithTimepoint(timepoint.timepointId, title);
+}

Packages/lesiontracker/package.js

@@ -10,16 +10,28 @@ Package.onUse(function(api) {
     api.use('standard-app-packages');
     api.use('jquery');
     api.use('stylus');
+
+    // Control over logging
     api.use('practicalmeteor:loglevel');
 
+    // Unique IDs
+    api.use('rwatts:uuid');
+
+    // Template overriding
+    api.use('aldeed:template-extension@4.0.0');
+
     // Our custom package
+    api.use('worklist');
     api.use('cornerstone');
 
     api.addFiles('log.js', [ 'client', 'server' ]);
 
+    // Client-side collections
     api.addFiles('client/collections/LesionLocations.js', 'client');
     api.addFiles('client/collections/LocationResponses.js', 'client');
+    api.addFiles('client/collections/PatientLocations.js', 'client');
 
+    // Additional Custom Cornerstone Tools for Lesion Tracker
     api.addFiles('client/compatibility/lesionTool.js', 'client', {
         bare: true
     });
@@ -32,14 +44,27 @@ Package.onUse(function(api) {
     api.addFiles('client/compatibility/deleteLesionKeyboardTool.js', 'client', {
         bare: true
     });
-    api.addFiles('client/compatibility/LesionManager.js', 'client', {
+
+    // Trial Criteria data validation (the Meteor package is currently out-of-date)
+    api.addFiles('client/compatibility/validate.js', 'client', {
         bare: true
     });
 
+    // UI Components
+    api.addFiles('client/components/lesionTrackerLayout/lesionTrackerLayout.html', 'client');
+    api.addFiles('client/components/lesionTrackerLayout/lesionTrackerLayout.styl', 'client');
+
     api.addFiles('client/components/associationModal/associationModal.html', 'client');
     api.addFiles('client/components/associationModal/associationModal.styl', 'client');
     api.addFiles('client/components/associationModal/associationModal.js', 'client');
 
+    api.addFiles('client/components/optionsButton/optionsButton.html', 'client');
+    api.addFiles('client/components/optionsButton/optionsButton.styl', 'client');
+
+    api.addFiles('client/components/optionsModal/optionsModal.html', 'client');
+    api.addFiles('client/components/optionsModal/optionsModal.styl', 'client');
+    api.addFiles('client/components/optionsModal/optionsModal.js', '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');
@@ -56,8 +81,8 @@ Package.onUse(function(api) {
     api.addFiles('client/components/lesionTableTimepointCell/lesionTableTimepointCell.js', 'client');
 
     api.addFiles('client/components/lesionTableTimepointHeader/lesionTableTimepointHeader.html', 'client');
-    api.addFiles('client/components/lesionTableTimepointHeader/lesionTableTimepointHeader.js', 'client');
     api.addFiles('client/components/lesionTableTimepointHeader/lesionTableTimepointHeader.styl', 'client');
+    api.addFiles('client/components/lesionTableTimepointHeader/lesionTableTimepointHeader.js', 'client');
 
     api.addFiles('client/components/nonTargetLesionDialog/nonTargetLesionDialog.html', 'client');
     api.addFiles('client/components/nonTargetLesionDialog/nonTargetLesionDialog.styl', 'client');
@@ -75,6 +100,10 @@ Package.onUse(function(api) {
     api.addFiles('client/components/confirmDeleteDialog/confirmDeleteDialog.styl', 'client');
     api.addFiles('client/components/confirmDeleteDialog/confirmDeleteDialog.js', 'client');
 
+    api.addFiles('client/components/conformanceCheckFeedback/conformanceCheckFeedback.html', 'client');
+    api.addFiles('client/components/conformanceCheckFeedback/conformanceCheckFeedback.styl', 'client');
+    api.addFiles('client/components/conformanceCheckFeedback/conformanceCheckFeedback.js', 'client');
+
     api.addFiles('client/components/nonTargetResponseDialog/nonTargetResponseDialog.html', 'client');
     api.addFiles('client/components/nonTargetResponseDialog/nonTargetResponseDialog.styl', 'client');
     api.addFiles('client/components/nonTargetResponseDialog/nonTargetResponseDialog.js', 'client');
@@ -82,6 +111,17 @@ Package.onUse(function(api) {
     api.addFiles('client/components/timepointTextDialog/timepointTextDialog.html', 'client');
     api.addFiles('client/components/timepointTextDialog/timepointTextDialog.styl', 'client');
 
+    api.addFiles('client/components/lesionTrackerWorklistStudy/lesionTrackerWorklistStudy.html', 'client');
+    api.addFiles('client/components/lesionTrackerWorklistStudy/lesionTrackerWorklistStudy.styl', 'client');
+    api.addFiles('client/components/lesionTrackerWorklistStudy/lesionTrackerWorklistStudy.js', 'client');
+
+    api.addFiles('client/components/lesionTrackerWorklistContextMenu/lesionTrackerWorklistContextMenu.html', 'client');
+    api.addFiles('client/components/lesionTrackerWorklistContextMenu/lesionTrackerWorklistContextMenu.js', 'client');
+
+    api.addFiles('client/components/lesionTrackerViewportOverlay/lesionTrackerViewportOverlay.html', 'client');
+    api.addFiles('client/components/lesionTrackerViewportOverlay/lesionTrackerViewportOverlay.styl', 'client');
+    api.addFiles('client/components/lesionTrackerViewportOverlay/lesionTrackerViewportOverlay.js', 'client');
+
     // Server functions
     api.addFiles('server/collections.js', 'server');
     api.addFiles('server/removeCollections.js', [ 'server' ]);
@@ -89,34 +129,67 @@ Package.onUse(function(api) {
     // Both client and server functions
     api.addFiles('both/collections.js', [ 'client', 'server' ]);
 
+    // Worklist-related functions
+    api.addFiles('lib/worklist/openNewTabWithTimepoint.js', 'client');
+    api.addFiles('lib/worklist/worklistModification.js', 'client');
+
     // Library functions
-    api.addFiles('lib/uuid.js', 'client');
+    api.addFiles('lib/TrialCriteriaConstraints.js', 'client');
+    api.addFiles('lib/TrialResponseCriteria.js', 'client');
+    api.addFiles('lib/LesionManager.js', 'client');
+    api.addFiles('lib/pixelSpacingAutorunCheck.js', 'client');
     api.addFiles('lib/toggleLesionTrackerTools.js', 'client');
     api.addFiles('lib/clearMeasurementTimepointData.js', 'client');
     api.addFiles('lib/removeToolDataWithMeasurementId.js', 'client');
     api.addFiles('lib/getTimepointObject.js', 'client');
+    api.addFiles('lib/getTimepointName.js', 'client');
     api.addFiles('lib/activateMeasurements.js', 'client');
     api.addFiles('lib/activateLesion.js', 'client');
     api.addFiles('lib/deactivateAllToolData.js', 'client');
     api.addFiles('lib/clearTools.js', 'client');
+    api.addFiles('lib/calculateTotalLesionBurden.js', 'client');
+
+    api.addFiles('lib/syncMeasurementAndToolData.js', 'client');
+    api.addFiles('lib/updateRelatedElements.js', 'client');
+
+    api.addFiles('lib/handleMeasurementAdded.js', 'client');
+    api.addFiles('lib/handleMeasurementModified.js', 'client');
+    api.addFiles('lib/handleMeasurementRemoved.js', 'client');
+
 
     // Export global functions
-    api.export('activateLesion','client');
+    api.export('pixelSpacingAutorunCheck', 'client');
-    api.export('activateMeasurements','client');
+    api.export('handleMeasurementAdded', 'client');
-    api.export('deactivateAllToolData','client');
+    api.export('handleMeasurementModified', 'client');
+    api.export('handleMeasurementRemoved', 'client');
+    api.export('syncMeasurementAndToolData', 'client');
+    api.export('updateRelatedElements', 'client');
+    api.export('openNewTabWithTimepoint', 'client');
+    api.export('activateLesion', 'client');
+    api.export('activateMeasurements', 'client');
+    api.export('deactivateAllToolData', 'client');
     api.export('toggleLesionTrackerTools', 'client');
     api.export('clearMeasurementTimepointData', 'client');
     api.export('removeToolDataWithMeasurementId', 'client');
     api.export('getTimepointObject', 'client');
     api.export('clearTools', 'client');
+    api.export('getTimepointName', 'client');
+    api.export('getTrialCriteriaConstraints', 'client');
+    api.export('calculateTotalLesionBurden', 'client');
+
+    // Export global objects
+    api.export('TrialResponseCriteria', 'client');
+    api.export('TrialCriteriaConstraints', 'client');
     api.export('LesionManager', 'client');
 
     // Export client-side collections
+    api.export('ValidationErrors', 'client');
     api.export('LesionLocations', 'client');
     api.export('LocationResponses', 'client');
     api.export('PatientLocations', 'client');
 
     // Export collections spanning both client and server
     api.export('Measurements', [ 'client', 'server' ]);
+    api.export('Studies', [ 'client', 'server' ]);
     api.export('Timepoints', [ 'client', 'server' ]);
 });

Packages/lesiontracker/server/collections.js

@@ -1,10 +1,18 @@
-Meteor.publish('timepoints', function(patientId) {
+Meteor.publish('timepoints', function() {
+    return Timepoints.find();
+});
+
+Meteor.publish('singlePatientTimepoints', function(patientId) {
     return Timepoints.find({
         patientId: patientId
     });
 });
 
-Meteor.publish('measurements', function(patientId) {
+Meteor.publish('studies', function() {
+    return Studies.find();
+});
+
+Meteor.publish('singlePatientMeasurements', function(patientId) {
     return Measurements.find({
         patientId: patientId
     });

Packages/lesiontracker/server/removeCollections.js

@@ -43,5 +43,11 @@ Meteor.methods({
         Measurements.remove({
             patientId: patientId
         });
+    },
+    clearAllTimepoints: function() {
+        Timepoints.remove({});
+    },
+    removeTimepoint: function(id) {
+        Timepoints.remove(id);
     }
 });

Packages/viewerbase/client/components/viewer/viewportOverlay/viewportOverlay.js

@@ -10,7 +10,7 @@ function getElementIfNotEmpty(viewportIndex) {
         element = imageViewerViewports.get(viewportIndex),
         canvases = imageViewerViewports.eq(viewportIndex).find('canvas');
 
-    if (!element || $(element).hasClass("empty") || canvases.length === 0) {
+    if (!element || $(element).hasClass('empty') || canvases.length === 0) {
         return;
     }
 
@@ -20,6 +20,7 @@ function getElementIfNotEmpty(viewportIndex) {
     } catch(error) {
         return;
     }
+
     return element;
 }
 
@@ -28,10 +29,12 @@ function getPatient(property) {
     if (!this.imageId) {
         return false;
     }
+
     var patient = cornerstoneTools.metaData.get('patient', this.imageId);
     if (!patient) {
         return '';
     }
+
     return patient[property];
 }
 
@@ -40,10 +43,12 @@ function getStudy(property) {
     if (!this.imageId) {
         return false;
     }
+
     var study = cornerstoneTools.metaData.get('study', this.imageId);
     if (!study) {
         return '';
     }
+
     return study[property];
 }
 
@@ -52,10 +57,12 @@ function getSeries(property) {
     if (!this.imageId) {
         return false;
     }
+
     var series = cornerstoneTools.metaData.get('series', this.imageId);
     if (!series) {
         return '';
     }
+
     return series[property];
 }
 
@@ -64,10 +71,12 @@ function getInstance(property) {
     if (!this.imageId) {
         return false;
     }
+
     var instance = cornerstoneTools.metaData.get('instance', this.imageId);
     if (!instance) {
         return '';
     }
+
     return instance[property];
 }
 
@@ -76,15 +85,18 @@ function getImage(viewportIndex) {
     if (!element) {
         return false;
     }
+
     var enabledElement;
     try {
         enabledElement = cornerstone.getEnabledElement(element);
     } catch(error) {
         return false;
     }
+
     if (!enabledElement || !enabledElement.image) {
         return false;
     }
+
     return enabledElement.image;
 }
 
@@ -95,10 +107,12 @@ Template.viewportOverlay.helpers({
         if (!element) {
             return '';
         }
+
         var viewport = cornerstone.getViewport(element);
         if (!viewport) {
             return '';
         }
+
         return 'W ' + viewport.voi.windowWidth.toFixed(0) + ' L ' + viewport.voi.windowCenter.toFixed(0);
     },
     zoom: function() {
@@ -107,10 +121,12 @@ Template.viewportOverlay.helpers({
         if (!element) {
             return '';
         }
+
         var viewport = cornerstone.getViewport(element);
         if (!viewport) {
             return '';
         }
+
         return (viewport.scale * 100.0);
     },
     imageDimensions: function() {
@@ -120,39 +136,40 @@ Template.viewportOverlay.helpers({
         if (!image) {
             return '';
         }
+
         return image.width + ' x ' + image.height;
     },
-    patientName : function() {
+    patientName: function() {
         return getPatient.call(this, 'name');
     },
-    patientId : function() {
+    patientId: function() {
         return getPatient.call(this, 'id');
     },
-    studyDate : function() {
+    studyDate: function() {
         return getStudy.call(this, 'studyDate');
     },
-    studyTime : function() {
+    studyTime: function() {
         return getStudy.call(this, 'studyTime');
     },
-    studyDescription : function() {
+    studyDescription: function() {
         return getStudy.call(this, 'studyDescription');
     },
-    seriesDescription : function() {
+    seriesDescription: function() {
         return getSeries.call(this, 'seriesDescription');
     },
-    seriesNumber : function() {
+    seriesNumber: function() {
         return getSeries.call(this, 'seriesNumber');
     },
-    imageNumber : function() {
+    imageNumber: function() {
         return getInstance.call(this, 'instanceNumber');
     },
-    imageIndex : function() {
+    imageIndex: function() {
         return getInstance.call(this, 'index');
     },
-    numImages : function() {
+    numImages: function() {
         return getSeries.call(this, 'numImages');
     },
-    prior : function() {
+    prior: function() {
         // This helper is updated whenever a new image is displayed in the viewport
         Session.get('CornerstoneNewImage' + this.viewportIndex);
         if (!this.imageId) {
@@ -165,14 +182,18 @@ Template.viewportOverlay.helpers({
         // that we can obtain the oldest study as the first element of the array
         //
         // TODO= Find out if we should encode studyDate as a Date in the ViewerStudies Collection
-        var viewportStudies = ViewerStudies.find({}, {sort: {studyDate: 1}});
+        var viewportStudies = ViewerStudies.find({}, {
+            sort: {
+                studyDate: 1
+            }
+        });
         if (viewportStudies.count() < 2) {
             return;
         }
 
         // Get study data
         var study = cornerstoneTools.metaData.get('study', this.imageId);
-        if (study.studyInstanceUid === viewportStudies.fetch()[0].studyInstanceUid) {
+        if (study.studyDate === viewportStudies.fetch()[0].studyDate) {
             return 'Prior';
         }
     }

Packages/viewerbase/client/components/viewer/viewportOverlay/viewportOverlay.styl

@@ -1,6 +1,7 @@
 .imageViewerViewportOverlay
+  font-family: Helvetica, OpenSans
   font-size: 13px
-  color: #e4ad00
+  color: #979797
   line-height: 18px
   display: none // Shown when an image is loaded
 

Packages/viewerbase/lib/enableHotkeys.js

@@ -7,40 +7,55 @@ Meteor.startup(function() {
     }
 
     OHIF.viewer.defaultHotkeys = {
-        defaultTool: "ESC",
+        defaultTool: 'ESC',
-        angle: "A",
+        angle: 'A',
-        stackScroll: "S",
+        stackScroll: 'S',
-        pan: "P",
+        pan: 'P',
-        magnify: "M",
+        magnify: 'M',
-        scrollDown: ["DOWN", "PAGEDOWN"],
+        scrollDown: ['DOWN', 'PAGEDOWN'],
-        scrollUp: ["UP", "PAGEUP"],
+        scrollUp: ['UP', 'PAGEUP'],
-        nextPanel: "RIGHT",
+        nextPanel: 'RIGHT',
-        previousPanel: "LEFT",
+        previousPanel: 'LEFT',
-        invert: "I",
+        invert: 'I',
-        flipV: "V",
+        flipV: 'V',
-        flipH: "H",
+        flipH: 'H',
-        wwwc: "W",
+        wwwc: 'W',
-        zoom: "Z",
+        zoom: 'Z',
-        cinePlay: "SPACE",
+        cinePlay: 'SPACE',
-        rotateR: "R",
+        rotateR: 'R',
-        rotateL: "L",
+        rotateL: 'L',
         toggleOverlayTags: 'SHIFT',
-        WLPresetSoftTissue: ["NUMPAD1", "1"],
+        WLPresetSoftTissue: ['NUMPAD1', '1'],
-        WLPresetLung: ["NUMPAD2", "2"],
+        WLPresetLung: ['NUMPAD2', '2'],
-        WLPresetLiver: ["NUMPAD3", "3"],
+        WLPresetLiver: ['NUMPAD3', '3'],
-        WLPresetBone: ["NUMPAD4", "4"],
+        WLPresetBone: ['NUMPAD4', '4'],
-        WLPresetBrain: ["NUMPAD5", "5"]
+        WLPresetBrain: ['NUMPAD5', '5']
     };
     
     // For now
     OHIF.viewer.hotkeys = OHIF.viewer.defaultHotkeys;
 
     OHIF.viewer.defaultWLPresets = {
-        'SoftTissue' : {wc : 40, ww : 400},
+        SoftTissue: {
-        'Lung' : {wc : -600, ww : 1500},
+            wc: 40,
-        'Liver' : {wc : 90, ww : 150},
+            ww: 400
-        'Bone' : {wc: 480, ww : 2500},
+        },
-        'Brain' : {wc : 40, ww : 80}
+        Lung: {
+            wc: -600,
+            ww: 1500
+        },
+        Liver: {
+            wc: 90,
+            ww: 150
+        },
+        Bone: {
+            wc: 480,
+            ww: 2500
+        },
+        Brain: {
+            wc: 40,
+            ww: 80
+        }
     };
 
     // For now
@@ -48,53 +63,53 @@ Meteor.startup(function() {
 
     OHIF.viewer.hotkeyFunctions = {
         wwwc: function() {
-            toolManager.setActiveTool("wwwc");
+            toolManager.setActiveTool('wwwc');
         },
         zoom: function() {
-            toolManager.setActiveTool("zoom");
+            toolManager.setActiveTool('zoom');
         },
         angle: function() {
-            toolManager.setActiveTool("angle");
+            toolManager.setActiveTool('angle');
         },
         dragProbe: function() {
-            toolManager.setActiveTool("dragProbe");
+            toolManager.setActiveTool('dragProbe');
         },
         ellipticalRoi: function() {
-            toolManager.setActiveTool("ellipticalRoi");
+            toolManager.setActiveTool('ellipticalRoi');
         },
         magnify: function() {
-            toolManager.setActiveTool("magnify");
+            toolManager.setActiveTool('magnify');
         },
         annotate: function() {
-            toolManager.setActiveTool("annotate");
+            toolManager.setActiveTool('annotate');
         },
         stackScroll: function() {
-            toolManager.setActiveTool("stackScroll");
+            toolManager.setActiveTool('stackScroll');
         },
         pan: function() {
-            toolManager.setActiveTool("pan");
+            toolManager.setActiveTool('pan');
         },
         length: function() {
-            toolManager.setActiveTool("length");
+            toolManager.setActiveTool('length');
         },
         spine: function() {
-            toolManager.setActiveTool("spine");
+            toolManager.setActiveTool('spine');
         },
         wwwcRegion: function() {
-            toolManager.setActiveTool("wwwcRegion");
+            toolManager.setActiveTool('wwwcRegion');
         },
-        zoomIn: function () {
+        zoomIn: function() {
-            var button = document.getElementById("zoomIn");
+            var button = document.getElementById('zoomIn');
             flashButton(button);
             zoomIn();
         },
-        zoomOut: function () {
+        zoomOut: function() {
-            var button = document.getElementById("zoomOut");
+            var button = document.getElementById('zoomOut');
             flashButton(button);
             zoomOut();
         },
-        zoomToFit: function () {
+        zoomToFit: function() {
-            var button = document.getElementById("zoomToFit");
+            var button = document.getElementById('zoomToFit');
             flashButton(button);
             zoomToFit();
         },
@@ -134,27 +149,27 @@ Meteor.startup(function() {
             previousActivePanel();
         },
         invert: function() {
-            var button = document.getElementById("invert");
+            var button = document.getElementById('invert');
             flashButton(button);
             invert();
         },
         flipV: function() {
-            var button = document.getElementById("flipV");
+            var button = document.getElementById('flipV');
             flashButton(button);
             flipV();
         },
         flipH: function() {
-            var button = document.getElementById("flipH");
+            var button = document.getElementById('flipH');
             flashButton(button);
             flipH();
         },
         rotateR: function() {
-            var button = document.getElementById("rotateR");
+            var button = document.getElementById('rotateR');
             flashButton(button);
             rotateR();
         },
         rotateL: function() {
-            var button = document.getElementById("rotateL");
+            var button = document.getElementById('rotateL');
             flashButton(button);
             rotateL();
         },
@@ -174,6 +189,8 @@ Meteor.startup(function() {
             }
         }
     };
+
+    OHIF.viewer.loadedSeriesData = {};
 });
 
 // Define a jQuery reverse function
@@ -198,7 +215,6 @@ function previousActivePanel() {
     setActiveViewport(element);
 }
 
-
 function nextActivePanel() {
     log.info('nextActivePanel');
     var currentIndex = Session.get('activeViewport');
@@ -224,7 +240,7 @@ function flashButton(button) {
     }
 
     button.classList.add('active');
-    setTimeout(function () {
+    setTimeout(function() {
         button.classList.remove('active');
     }, 100);
 }
@@ -233,13 +249,13 @@ function bindHotkey(hotkey, task) {
     var hotkeyFunctions = OHIF.viewer.hotkeyFunctions;
 
     // Only bind defined, non-empty HotKeys
-    if (!hotkey || hotkey === "") {
+    if (!hotkey || hotkey === '') {
         return;
     }
 
     var fn;
-    if (task.indexOf("WLPreset") > -1) {
+    if (task.indexOf('WLPreset') > -1) {
-        var presetName = task.replace("WLPreset", "");
+        var presetName = task.replace('WLPreset', '');
         fn = function() {
             applyWLPresetToActiveElement(presetName);
         };

Packages/viewerbase/lib/getWADORSImageId.js

@@ -29,8 +29,14 @@ getWADORSImageId = function(instance) {
         //maxPixelValue : 255,
         slope: instance.rescaleSlope,
         intercept: instance.rescaleIntercept,
-        windowCenter : windowCenter,
+        samplesPerPixel: instance.samplesPerPixel,
-        windowWidth : windowWidth,
+        imageOrientationPatient: instance.imageOrientationPatient,
+        imagePositionPatient: instance.imagePositionPatient,
+        sopClassUid: instance.sopClassUid,
+        instanceNumber: instance.instanceNumber,
+        frameOfReferenceUID: instance.frameOfReferenceUID,
+        windowCenter: windowCenter,
+        windowWidth: windowWidth,
         //render: cornerstone.renderColorImage,
         //getPixelData: getPixelData,
         //getImageData: getImageData,
@@ -47,6 +53,8 @@ getWADORSImageId = function(instance) {
         instance: instance
     };
 
-    var imageId = cornerstoneWADORSImageLoader.addImage(image);
+    var imageId = cornerstoneWADOImageLoader.imageManager.add(image);
+
+    console.log('WADO-RS ImageID: ' + imageId);
     return imageId;
 };

Packages/viewerbase/lib/helpers/formatPN.js

@@ -1,9 +1,14 @@
+/**
+ * Formats a patient name for display purposes
+ */
+formatPN = function(context) {
+    if (!context) {
+        return;
+    }
+    return context.replace('^', ', ');
+};
+
 /**
  * A global Blaze UI helper to format a patient name for display purposes
  */
-UI.registerHelper('formatPN', function (context) {
+UI.registerHelper('formatPN', formatPN);
-    if (!context) {
-        return undefined;
-    }
-    return context.replace('^', ', ');
-});