Work on refactoring measurements out of Lesion Tracker package

- Removed AssociatedStudies Collection
- Measurement API is generated from configuration files
- Data exchange methods are defined in configuration

LesionTracker/.meteor/packages

@@ -28,17 +28,19 @@ clinical:hipaa-logger
 
 aldeed:simple-schema          # Third party package to deal with schemas
 
+# OHIF Packages
 design
 ohif:core
+ohif:cornerstone
+ohif:viewerbase
+ohif:study-list
+ohif:dicom-services
+ohif:hanging-protocols
+ohif:user-management
+ohif:lesiontracker
 
-insecure@1.0.7                # Allow all DB writes from clients (for prototyping)
-cornerstone
-worklist
-viewerbase
-dicomweb
 accounts-base@1.2.14
 accounts-password@1.3.1
-
 ian:accounts-ui-bootstrap-3
 twbs:bootstrap
 http@1.2.10
@@ -49,7 +51,6 @@ fortawesome:fontawesome
 random@1.0.10
 reactive-var@1.0.11
 reactive-dict@1.1.8
-lesiontracker
 practicalmeteor:loglevel
 momentjs:moment
 
@@ -61,10 +62,10 @@ gilbertwat:bootstrap3-daterangepicker
 email@1.1.18
 peppelg:bootstrap-3-modal
 simple:reactive-method
-hangingprotocols
 fastclick@1.0.13
 standard-minifier-css@1.3.2
 standard-minifier-js@1.2.1
 johdirr:meteor-git-rev
 u2622:persistent-session
 shell-server@0.2.1
+aldeed:collection2

LesionTracker/.meteor/versions

@@ -1,5 +1,9 @@
 accounts-base@1.2.14
 accounts-password@1.3.1
+aldeed:collection2@2.10.0
+aldeed:collection2-core@1.2.0
+aldeed:schema-deny@1.1.0
+aldeed:schema-index@1.1.1
 aldeed:simple-schema@1.5.3
 aldeed:template-extension@4.0.0
 allow-deny@1.0.5
@@ -9,10 +13,10 @@ anti:i18n@0.4.3
 arsnebula:reactive-promise@0.9.1
 autoupdate@1.3.12
 babel-compiler@6.13.0
-babel-runtime@0.1.12
+babel-runtime@0.1.13
 base64@1.0.10
 binary-heap@1.0.10
-blaze@2.1.9
+blaze@2.2.0
 blaze-html-templates@1.0.5
 blaze-tools@1.0.10
 boilerplate-generator@1.0.11
@@ -33,7 +37,6 @@ clinical:router-middleware-stack@2.1.2
 clinical:router-url@2.1.0
 clinical:theming@0.4.10
 coffeescript@1.11.1_2
-cornerstone@0.0.1
 ddp@1.2.5
 ddp-client@1.3.2
 ddp-common@1.2.7
@@ -41,9 +44,7 @@ ddp-rate-limiter@1.0.6
 ddp-server@1.3.11
 deps@1.0.12
 design@0.0.1
-dicomweb@0.0.1
 diff-sequence@1.0.7
-dimseservice@0.0.1
 ecmascript@0.5.9
 ecmascript-runtime@0.3.15
 ejson@1.0.13
@@ -54,14 +55,12 @@ fortawesome:fontawesome@4.6.3
 geojson-utils@1.0.10
 gilbertwat:bootstrap3-daterangepicker@1.3.21_1
 grove:less@0.2.0
-hangingprotocols@0.0.1
 hot-code-push@1.0.4
 html-tools@1.0.11
 htmljs@1.0.11
 http@1.2.10
 ian:accounts-ui-bootstrap-3@1.2.89
 id-map@1.0.9
-insecure@1.0.7
 iron:controller@1.0.12
 iron:core@1.0.11
 iron:dynamic-template@1.0.12
@@ -69,7 +68,6 @@ iron:layout@1.0.12
 johdirr:meteor-git-rev@0.0.4
 jquery@1.11.10
 launch-screen@1.1.0
-lesiontracker@0.0.1
 livedata@1.0.18
 localstorage@1.0.12
 logging@1.1.16
@@ -93,12 +91,21 @@ npm-bcrypt@0.9.2
 npm-mongo@2.2.11_2
 observe-sequence@1.0.14
 ohif:core@0.0.1
+ohif:cornerstone@0.0.1
+ohif:dicom-services@0.0.1
+ohif:hanging-protocols@0.0.1
+ohif:lesiontracker@0.0.1
+ohif:measurements@0.0.1
+ohif:study-list@0.0.1
+ohif:user-management@0.0.1
+ohif:viewerbase@0.0.1
+ohif:wadoproxy@0.0.1
 ordered-dict@1.0.9
-orthanc-remote@0.0.1
 peppelg:bootstrap-3-modal@1.0.4
 practicalmeteor:chai@2.1.0_1
 practicalmeteor:loglevel@1.2.0_2
 promise@0.8.8
+raix:eventemitter@0.1.3
 random@1.0.10
 rate-limit@1.0.6
 reactive-dict@1.1.8
@@ -106,7 +113,6 @@ reactive-var@1.0.11
 reload@1.1.11
 retry@1.0.9
 routepolicy@1.0.12
-rwatts:uuid@0.1.0
 service-configuration@1.0.11
 session@1.1.7
 sha@1.0.9
@@ -133,9 +139,6 @@ ui@1.0.12
 underscore@1.0.10
 url@1.0.11
 validatejs@0.0.1
-viewerbase@0.0.1
-wadoproxy@0.0.1
 webapp@1.3.12
 webapp-hashing@1.0.9
-worklist@0.0.1
 zuuk:stale-session@1.0.8

LesionTracker/client/components/app/app.html

@@ -1,11 +1,11 @@
-<template name="lesionTracker">
+<template name="app">
     <div class="topBar noselect {{#if onStudyList}}studyList{{/if}}">
         <div class="clearfix p-x-1 p-t-1">
             <a target='_blank'
                class="brandSection pull-left"
                href="http://ohif.org">
                 <svg class="logoImage">
-                    <use xlink:href="/packages/viewerbase/assets/icons.svg#icon-ohif-logo"></use>
+                    <use xlink:href="/packages/ohif_viewerbase/assets/icons.svg#icon-ohif-logo"></use>
                 </svg>
                 <div class="logoText">
                     Open Health Imaging Foundation
@@ -22,10 +22,10 @@
         </div>
     </div>
     {{ >timeoutCountdownDialog }}
-    <div id="worklistTabs" class="tab-content">
+    <div id="studylistTabs" class="tab-content">
-        <div class="tab-pane active" id="worklistTab">
+        <div class="tab-pane active" id="studylistTab">
-            <div class="worklistContainer">
+            <div class="studylistContainer">
-                {{> worklistResult }}
+                {{> studylistResult }}
             </div>
         </div>
         <div class="tab-pane" id="viewerTab">
@@ -37,6 +37,6 @@
     {{ >confirmRemoveTimepointAssociation }}
     {{ >lastLoginModal }}
     {{ >studyContextMenu }}
-    {{ >progressDialog}}
+    {{ >progressDialog }}
     {{ >viewSeriesDetailsModal }}
 </template>

LesionTracker/client/components/app/app.js

@@ -1,26 +1,26 @@
-const worklistContentId = 'worklistTab';
+const studylistContentId = 'studylistTab';
 const viewerContentId = 'viewerTab';
 
 // Define the ViewerData global object
 // If there is currently any Session data for this object,
 // use this to repopulate the variable
-Template.lesionTracker.onCreated(() => {
+Template.app.onCreated(() => {
     ViewerData = Session.get('ViewerData') || {};
 });
 
-Template.lesionTracker.events({
+Template.app.events({
     'click .js-toggle-studyList'() {
         const contentId = Session.get('activeContentId');
 
-        if (contentId !== worklistContentId) {
+        if (contentId !== studylistContentId) {
-            switchToTab(worklistContentId);
+            switchToTab(studylistContentId);
         } else {
             switchToTab(viewerContentId);
         }
     }
 });
 
-Template.lesionTracker.helpers({
+Template.app.helpers({
     studyListToggleText() {
         const contentId = Session.get('activeContentId');
         
@@ -31,7 +31,7 @@ Template.lesionTracker.helpers({
             return;
         }
 
-        if (contentId === worklistContentId) {
+        if (contentId === studylistContentId) {
             return 'Back to viewer';
         } else if (contentId === viewerContentId) {
             return 'Study list';
@@ -39,7 +39,7 @@ Template.lesionTracker.helpers({
     },
 
     onStudyList() {
-        return (Session.get('activeContentId') === 'worklistTab');
+        return (Session.get('activeContentId') === 'studylistTab');
     }
 });
 

LesionTracker/client/components/app/app.styl

@@ -69,7 +69,7 @@ $expandedHeight = 160px
       top: 5px
       left: 5px
 
-#worklistTabs
+#studylistTabs
   height: "calc(100% - %s)" % $topBarHeight
 
   .tab-pane

LesionTracker/client/components/toolbarSection/toolbarSection.html

@@ -20,10 +20,10 @@
             <div class="pull-right m-t-1 rm-x-1">
                 {{>roundedButtonGroup rightSidebarToggleButtonData}}
             </div>
-            <div id="toggleHUD" class="toolbarSectionButton pull-right rp-x-1 m-t-1 rm-r-3 {{#if session 'lesionTableHudOpen'}}active{{/if}}">
+            <div id="toggleHUD" class="toolbarSectionButton pull-right rp-x-1 m-t-1 rm-r-3 {{#if session 'measurementTableHudOpen'}}active{{/if}}">
                 <div class="svgContainer">
                     <svg>
-                        <use xlink:href="/packages/viewerbase/assets/icons.svg#icon-hud"></use>
+                        <use xlink:href="/packages/ohif_viewerbase/assets/icons.svg#icon-hud"></use>
                     </svg>
                 </div>
                 <div class="buttonLabel">HUD</div>
@@ -31,7 +31,7 @@
             <div class="toolbarSectionButton pull-right rp-x-1 m-t-1 rm-r-1" data-toggle="modal" data-target="#optionsModal">
                 <div class="svgContainer">
                     <svg>
-                        <use xlink:href="/packages/viewerbase/assets/icons.svg#icon-trial-info"></use>
+                        <use xlink:href="/packages/ohif_viewerbase/assets/icons.svg#icon-trial-info"></use>
                     </svg>
                 </div>
                 <div class="buttonLabel">Trial</div>

LesionTracker/client/components/toolbarSection/toolbarSection.js

@@ -22,7 +22,7 @@ Template.toolbarSection.helpers({
             value: instance.data.state,
             options: [{
                 value: 'studies',
-                svgLink: '/packages/viewerbase/assets/icons.svg#icon-studies',
+                svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-studies',
                 svgWidth: 15,
                 svgHeight: 13,
                 bottomLabel: 'Studies'
@@ -37,75 +37,73 @@ Template.toolbarSection.helpers({
             key: 'rightSidebar',
             value: instance.data.state,
             options: [{
-                value: 'lesions',
+                value: 'measurements',
-                svgLink: '/packages/viewerbase/assets/icons.svg#icon-measurements-lesions',
+                svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-measurements-lesions',
                 svgWidth: 18,
                 svgHeight: 10,
-                bottomLabel: 'Lesions'
+                bottomLabel: 'Measurements'
-            }, {
-                value: 'additional',
-                svgLink: '/packages/viewerbase/assets/icons.svg#icon-measurements-additional',
-                svgWidth: 14,
-                svgHeight: 13,
-                bottomLabel: 'Additional'
             }]
         };
     },
 
     toolbarButtons() {
         // Check if the measure tools shall be disabled
-        const isMesureDisabled = !Template.instance().data.timepointApi.currentTimepointId;
+        const isToolDisabled = false; //!Template.instance().data.timepointApi;
+        
         const buttonData = [];
 
         buttonData.push({
             id: 'zoom',
             title: 'Zoom',
             classes: 'imageViewerTool',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-zoom'
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-zoom'
         });
 
         buttonData.push({
             id: 'wwwc',
             title: 'Levels',
             classes: 'imageViewerTool',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-levels'
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-levels'
         });
 
         buttonData.push({
             id: 'pan',
             title: 'Pan',
             classes: 'imageViewerTool',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-pan'
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-pan'
         });
 
+        /*
+        TODO: design the link functionality
+        Commenting this out until we build this tool
         buttonData.push({
             id: 'link',
             title: 'Link',
             classes: 'imageViewerCommand toolbarSectionButton',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-link'
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-link'
-        });
+        });*/
 
         buttonData.push({
             id: 'bidirectional',
             title: 'Target',
             classes: 'imageViewerTool rm-l-3',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-measure-target',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-target',
-            disabled: isMesureDisabled
+            disabled: isToolDisabled
         });
 
         buttonData.push({
             id: 'nonTarget',
             title: 'Non-Target',
             classes: 'imageViewerTool toolbarSectionButton',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-measure-non-target',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-non-target',
-            disabled: isMesureDisabled
+            disabled: isToolDisabled
         });
 
         buttonData.push({
             id: 'length',
             title: 'Temp',
             classes: 'imageViewerTool toolbarSectionButton',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-measure-temp'
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-temp'
         });
 
         return buttonData;
@@ -113,7 +111,7 @@ Template.toolbarSection.helpers({
 
     extraToolbarButtons() {
         // Check if the measure tools shall be disabled
-        const isMesureDisabled = !Template.instance().data.timepointApi.currentTimepointId;
+        const isToolDisabled = false; //!Template.instance().data.timepointApi.currentTimepointId;
         const buttonData = [];
 
         // TODO: Get real icons for CR / UN / EX
@@ -121,24 +119,24 @@ Template.toolbarSection.helpers({
             id: 'crTool',
             title: 'CR Tool',
             classes: 'imageViewerTool toolbarSectionButton',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-measure-temp',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-temp',
-            disabled: isMesureDisabled
+            disabled: isToolDisabled
         });
 
         buttonData.push({
             id: 'unTool',
             title: 'UN Tool',
             classes: 'imageViewerTool toolbarSectionButton',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-measure-temp',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-temp',
-            disabled: isMesureDisabled
+            disabled: isToolDisabled
         });
 
         buttonData.push({
             id: 'exTool',
             title: 'EX Tool',
             classes: 'imageViewerTool toolbarSectionButton',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-measure-temp',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-temp',
-            disabled: isMesureDisabled
+            disabled: isToolDisabled
         });
 
         return buttonData;
@@ -147,8 +145,8 @@ Template.toolbarSection.helpers({
 
 Template.toolbarSection.events({
     'click #toggleHUD'() {
-        const state = Session.get('lesionTableHudOpen');
+        const state = Session.get('measurementTableHudOpen');
-        Session.set('lesionTableHudOpen', !state);
+        Session.set('measurementTableHudOpen', !state);
     }
 });
 

LesionTracker/client/components/viewer/viewer.html

@@ -0,0 +1,17 @@
+<template name="viewer">
+    {{#if and Template.subscriptionsReady dataSourcesReady}}
+        <div class="viewerDialogs">
+            {{>confirmDeleteDialog}}
+            {{>measurementLocationDialog (clone this)}}
+            {{>nonTargetLesionDialog (clone this)}}
+            {{>nonTargetResponseDialog (clone this)}}
+            {{>measurementTableHUD (clone this)}}
+        </div>
+        <div id="viewer">
+            {{>toolbarSection (clone this)}}
+            {{>viewerSection (clone this)}}
+        </div>
+    {{else}}
+        {{>loadingText}}
+    {{/if}}
+</template>

LesionTracker/client/components/viewer/viewer.js

@@ -0,0 +1,113 @@
+import { OHIF } from 'meteor/ohif:core';
+import { TimepointsConfiguration } from 'meteor/ohif:measurements/both/configuration/timepoints';
+import { MeasurementsConfiguration } from 'meteor/ohif:measurements/both/configuration/measurements';
+import { MeasurementHandlers } from 'meteor/ohif:measurements/client/lib/MeasurementHandlers';
+
+Session.set('TimepointsReady', false);
+Session.set('MeasurementsReady', false);
+
+Template.viewer.onCreated(() => {
+    const TimepointApi = TimepointsConfiguration.getTimepointsApi();
+    const MeasurementApi = MeasurementsConfiguration.getMeasurementsApi();
+
+    OHIF.viewer = OHIF.viewer || {};
+    ViewerData = window.ViewerData || ViewerData;
+
+    const instance = Template.instance();
+
+    ValidationErrors.remove({});
+
+    instance.data.state = new ReactiveDict();
+    instance.data.state.set('leftSidebar', Session.get('leftSidebar'));
+    instance.data.state.set('rightSidebar', Session.get('rightSidebar'));
+
+    const contentId = instance.data.contentId;
+
+    OHIF.viewer.functionList = $.extend(OHIF.viewer.functionList, {
+        toggleLesionTrackerTools: toggleLesionTrackerTools,
+        clearTools: clearTools,
+        bidirectional: () => {
+            // Used for hotkeys
+            toolManager.setActiveTool('bidirectional');
+        },
+        nonTarget: () => {
+            // 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.bidirectional = 'T'; // Target
+    OHIF.viewer.defaultHotkeys.nonTarget = 'N'; // Non-target
+
+    if (ViewerData[contentId].loadedSeriesData) {
+        log.info('Reloading previous loadedSeriesData');
+        OHIF.viewer.loadedSeriesData = ViewerData[contentId].loadedSeriesData;
+
+    } else {
+        log.info('Setting default ViewerData');
+        OHIF.viewer.loadedSeriesData = {};
+        ViewerData[contentId].loadedSeriesData = {};
+        Session.set('ViewerData', ViewerData);
+    }
+
+    Session.set('activeViewport', ViewerData[contentId].activeViewport || false);
+
+    // Set lesion tool buttons as disabled if pixel spacing is not available for active element
+    instance.autorun(pixelSpacingAutorunCheck);
+
+    // Update the ViewerStudies collection with the loaded studies
+    ViewerStudies.remove({});
+
+    instance.data.studies.forEach(study => {
+        study.selected = true;
+        study.displaySets = createStacks(study);
+        ViewerStudies.insert(study);
+    });
+
+    if (instance.data.currentTimepointId) {
+        instance.data.timepointApi = new TimepointApi(instance.data.currentTimepointId);
+        const timepointsPromise = instance.data.timepointApi.retrieveTimepoints();
+        timepointsPromise.then(() => {
+            Session.set('TimepointsReady', true);
+        })
+
+        instance.data.measurementApi = new MeasurementApi(instance.data.currentTimepointId);
+        const measurementsPromise = instance.data.measurementApi.retrieveMeasurements();
+        measurementsPromise.then(() => {
+            Session.set('MeasurementsReady', true);
+
+            instance.data.measurementApi.syncMeasurementsAndToolData();
+        })
+
+        // Provide the necessary data to the Measurement API and Timepoint API
+        const prior = instance.data.timepointApi.prior();
+        if (prior) {
+            instance.data.measurementApi.priorTimepointId = prior.timepointId;
+        }
+    } else {
+        console.warn('No current timepoint specified');
+        instance.data.measurementApi = new MeasurementApi();
+    }
+});
+
+Template.viewer.helpers({
+    dataSourcesReady() {
+        // TODO: Find a better way to do this
+        return Session.get('TimepointsReady') && Session.get('MeasurementsReady');
+    }
+})
+
+Template.viewer.events({
+    'CornerstoneToolsMeasurementAdded .imageViewerViewport'(event, instance, eventData) {
+        MeasurementHandlers.onAdded(event, instance, eventData);
+    },
+    'CornerstoneToolsMeasurementModified .imageViewerViewport'(event, instance, eventData) {
+        MeasurementHandlers.onModified(event, instance, eventData);
+    },
+    'CornerstoneToolsMeasurementRemoved .imageViewerViewport'(event, instance, eventData) {
+        MeasurementHandlers.onRemoved(event, instance, eventData);
+    }
+});

LesionTracker/client/components/viewerSection/viewerSection.html

@@ -0,0 +1,13 @@
+<template name="viewerSection">
+    <div class="viewerSection">
+        <div class="sidebarMenu sidebar-left {{#if leftSidebarOpen}}sidebar-open{{/if}}">
+            {{>studyTimepointBrowser (clone this)}}
+        </div>
+        <div class="mainContent {{#if leftSidebarOpen}}sidebar-left-open{{/if}} {{#if rightSidebarOpen}}sidebar-right-open{{/if}}">
+            {{>viewerMain (clone this)}}
+        </div>
+        <div class="sidebarMenu sidebar-right {{#if rightSidebarOpen}}sidebar-open{{/if}}">
+            {{>measurementTable (clone this)}}
+        </div>
+    </div>
+</template>

LesionTracker/client/components/viewerSection/viewerSection.js

@@ -1,4 +1,4 @@
-Template.flexboxLayout.events({
+Template.viewerSection.events({
     'transitionend .sidebarMenu'(event) {
         if (!event.target.classList.contains('sidebarMenu')) {
             return;
@@ -8,20 +8,12 @@ Template.flexboxLayout.events({
     }
 });
 
-Template.flexboxLayout.helpers({
+Template.viewerSection.helpers({
     leftSidebarOpen() {
         return Template.instance().data.state.get('leftSidebar');
     },
 
-    lesionSidebarOpen() {
-        return Template.instance().data.state.get('rightSidebar') === 'lesions';
-    },
-
-    additionalFindingsSidebarOpen() {
-        return Template.instance().data.state.get('rightSidebar') === 'additional';
-    },
-
     rightSidebarOpen() {
-        return Template.instance().data.state.get('rightSidebar') !== null;
+        return Template.instance().data.state.get('rightSidebar');
     }
 });

LesionTracker/client/lesionTrackerHangingProtocol.js

@@ -164,20 +164,4 @@ Meteor.call('removeHangingProtocolByID', HP.lesionTrackerFollowupProtocol.id, fu
     HangingProtocols.insert(HP.lesionTrackerFollowupProtocol);
 });
 
-Meteor.startup(function() {
+HangingProtocols.insert(HP.defaultProtocol);
-    getTimepointType = function(study) {
-        var timepoint = Timepoints.findOne({
-            studyInstanceUids: {
-                $in: [study.studyInstanceUid]
-            }
-        });
-
-        if (!timepoint) {
-            return;
-        }
-
-        return timepoint.timepointType;
-    };
-
-    HP.addCustomAttribute('timepointType', 'Timepoint Type', getTimepointType);
-});

LesionTracker/client/routes.js

@@ -31,8 +31,8 @@ Router.route('/', function() {
         if (verifyEmail && Meteor.user().emails && !Meteor.user().emails[0].verified) {
             this.render('emailVerification', routerOptions);
         } else {
-            Session.set('activeContentId', 'worklistTab');
+            Session.set('activeContentId', 'studylistTab');
-            this.render('lesionTracker', routerOptions);
+            this.render('app', routerOptions);
         }
 
     } else {
@@ -46,16 +46,7 @@ Router.route('/viewer/timepoints/:_id', {
     onBeforeAction: function() {
         var timepointId = this.params._id;
 
-        // Check if this study is already loaded in a tab
+        this.render('app', routerOptions);
-        // If it is, stop here so we don't keep adding tabs on hot-code reloads
-        var tab = WorklistTabs.findOne({
-            timepointId: timepointId
-        });
-        if (tab) {
-            return;
-        }
-
-        this.render('lesionTracker', routerOptions);
         openNewTabWithTimepoint(timepointId);
     }
 });

LesionTracker/server/dropAllCollections.js

@@ -0,0 +1,14 @@
+// Temporary fix to drop all Collections on server restart
+// http://stackoverflow.com/questions/23891631/meteor-how-can-i-drop-all-mongo-collections-and-clear-all-data-on-startup
+Meteor.startup(() => {
+    console.warn('Dropping all Collections!');
+    Object.keys(global).forEach((key) => {
+        const object = global[key];
+        if (object instanceof Meteor.Collection) {
+            if (!(/^server|currentServer$/).test(object._name)) {
+                console.warn(`Dropping: ${object._debugName}`);
+                object.remove({});
+            }
+        }
+    });
+});

OHIFViewer/.meteor/packages

@@ -4,6 +4,16 @@
 # 'meteor add' and 'meteor remove' will edit this file for you,
 # but you can also edit it by hand.
 
+# OHIF Packages
+design
+ohif:core
+ohif:cornerstone
+ohif:viewerbase
+ohif:study-list
+ohif:dicom-services
+ohif:hanging-protocols
+# ohif:user-management
+
 twbs:bootstrap
 http@1.2.10
 arsnebula:reactive-promise
@@ -24,24 +34,17 @@ random@1.0.10
 ejson@1.0.13
 spacebars@1.0.12
 check@1.2.4
-cornerstone
-dicomweb
 aldeed:simple-schema          # Third party package to deal with schemas
-design
-ohif:core
 ecmascript@0.5.9
-viewerbase
-worklist
 reactive-var@1.0.11
+
 practicalmeteor:loglevel
-hangingprotocols
 reactive-dict@1.1.8
 clinical:router
 fastclick@1.0.13
 standard-minifier-css@1.3.2
 standard-minifier-js@1.2.1
 johdirr:meteor-git-rev
-wadoproxy
 aldeed:template-extension
 peppelg:bootstrap-3-modal
 shell-server@0.2.1

OHIFViewer/.meteor/versions

@@ -1,14 +1,18 @@
 accounts-base@1.2.14
+aldeed:collection2@2.10.0
+aldeed:collection2-core@1.2.0
+aldeed:schema-deny@1.1.0
+aldeed:schema-index@1.1.1
 aldeed:simple-schema@1.5.3
 aldeed:template-extension@4.0.0
 allow-deny@1.0.5
 arsnebula:reactive-promise@0.9.1
 autoupdate@1.3.12
 babel-compiler@6.13.0
-babel-runtime@0.1.12
+babel-runtime@0.1.13
 base64@1.0.10
 binary-heap@1.0.10
-blaze@2.1.9
+blaze@2.2.0
 blaze-html-templates@1.0.5
 blaze-tools@1.0.10
 boilerplate-generator@1.0.11
@@ -21,7 +25,6 @@ clinical:router-location@2.1.0
 clinical:router-middleware-stack@2.1.2
 clinical:router-url@2.1.0
 coffeescript@1.11.1_2
-cornerstone@0.0.1
 ddp@1.2.5
 ddp-client@1.3.2
 ddp-common@1.2.7
@@ -29,9 +32,7 @@ ddp-rate-limiter@1.0.6
 ddp-server@1.3.11
 deps@1.0.12
 design@0.0.1
-dicomweb@0.0.1
 diff-sequence@1.0.7
-dimseservice@0.0.1
 ecmascript@0.5.9
 ecmascript-runtime@0.3.15
 ejson@1.0.13
@@ -39,7 +40,6 @@ fastclick@1.0.13
 fortawesome:fontawesome@4.6.3
 geojson-utils@1.0.10
 gilbertwat:bootstrap3-daterangepicker@1.3.21_1
-hangingprotocols@0.0.1
 hot-code-push@1.0.4
 html-tools@1.0.11
 htmljs@1.0.11
@@ -74,12 +74,18 @@ natestrauser:select2@4.0.3
 npm-mongo@2.2.11_2
 observe-sequence@1.0.14
 ohif:core@0.0.1
+ohif:cornerstone@0.0.1
+ohif:dicom-services@0.0.1
+ohif:hanging-protocols@0.0.1
+ohif:study-list@0.0.1
+ohif:viewerbase@0.0.1
+ohif:wadoproxy@0.0.1
 ordered-dict@1.0.9
-orthanc-remote@0.0.1
 peppelg:bootstrap-3-modal@1.0.4
 practicalmeteor:chai@2.1.0_1
 practicalmeteor:loglevel@1.2.0_2
 promise@0.8.8
+raix:eventemitter@0.1.3
 random@1.0.10
 rate-limit@1.0.6
 reactive-dict@1.1.8
@@ -87,7 +93,6 @@ reactive-var@1.0.11
 reload@1.1.11
 retry@1.0.9
 routepolicy@1.0.12
-rwatts:uuid@0.1.0
 service-configuration@1.0.11
 session@1.1.7
 shell-server@0.2.1
@@ -108,8 +113,5 @@ ui@1.0.12
 underscore@1.0.10
 url@1.0.11
 validatejs@0.0.1
-viewerbase@0.0.1
-wadoproxy@0.0.1
 webapp@1.3.12
 webapp-hashing@1.0.9
-worklist@0.0.1

OHIFViewer/client/components/ohifViewer/ohifViewer.html

@@ -40,7 +40,7 @@
         </div>
     </div>
     {{>serverInformationModal}}
-    {{>worklist}}
+    {{>studylist}}
     {{>aboutModal}}
     {{>viewSeriesDetailsModal}}
 </template>

OHIFViewer/client/components/viewer/viewer.styl

@@ -1,5 +1,8 @@
 @import "{design}/app"
 
+body
+  background-color: black
+
 #viewer
   background-color: black
   height: 100%

OHIFViewer/client/routes.js

@@ -1,16 +1,5 @@
 Session.setDefault('ViewerData', {});
 
-// Re-add any tab data saved in the Session
-WorklistTabs.remove({});
-Object.keys(ViewerData).forEach(function(contentId) {
-    var tabData = ViewerData[contentId];
-    var data = {
-        title: tabData.title,
-        contentid: tabData.contentid
-    };
-    WorklistTabs.insert(data);
-});
-
 Router.configure({
     layoutTemplate: 'layout',
     loadingTemplate: 'layout'
@@ -31,16 +20,6 @@ Router.route('/viewer/:_id', {
     onBeforeAction: function() {
         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 tabs = WorklistTabs.find({
-            studyInstanceUid: studyInstanceUid
-        });
-
-        if (tabs.count()) {
-            return;
-        }
-
         this.render('ohifViewer', {
             data: function() {
                 return {

PETSUVMeasurements/.gagarin/.gitignore

@@ -0,0 +1 @@
+local

PETSUVMeasurements/.meteor/.finished-upgraders

@@ -0,0 +1,16 @@
+# This file contains information which helps Meteor properly upgrade your
+# app when you run 'meteor update'. You should check it into version control
+# with your project.
+
+notices-for-0.9.0
+notices-for-0.9.1
+0.9.4-platform-file
+notices-for-facebook-graph-api-2
+1.2.0-standard-minifiers-package
+1.2.0-meteor-platform-split
+1.2.0-cordova-changes
+1.2.0-breaking-changes
+1.3.0-split-minifiers-package
+1.3.5-remove-old-dev-bundle-link
+1.4.0-remove-old-dev-bundle-link
+1.4.1-add-shell-server-package

PETSUVMeasurements/.meteor/.gitignore

@@ -0,0 +1,2 @@
+dev_bundle
+local

PETSUVMeasurements/.meteor/.id

@@ -0,0 +1,7 @@
+# This file contains a token that is unique to your project.
+# Check it into your repository along with the rest of this directory.
+# It can be used for purposes such as:
+#   - ensuring you don't accidentally deploy one app on top of another
+#   - providing package authors with aggregated statistics
+
+1q3vtk41m2yk4k1rqj08l

PETSUVMeasurements/.meteor/nightwatch.json

@@ -0,0 +1,136 @@
+{
+  "starrynight": {
+    "version": "3.7.0"
+  },
+  "nightwatch": {
+    "version": "0.8.6"
+  },
+  "src_folders": [
+    "./tests/nightwatch/walkthroughs"
+  ],
+  "output_folder": "./tests/nightwatch/reports",
+  "custom_commands_path": [
+    "./tests/nightwatch/commands",
+    "./tests/nightwatch/commands/api/meteor",
+    "./tests/nightwatch/commands/actions",
+    "./tests/nightwatch/commands/components",
+    "./tests/nightwatch/commands/methods"
+  ],
+  "custom_assertions_path": [
+    "./tests/nightwatch/assertions"
+  ],
+  "globals_path": "./tests/nightwatch/globals.json",
+  "selenium": {
+    "start_process": true,
+    "server_path": "${npm_config_prefix}/lib/node_modules/starrynight/node_modules/selenium-server-standalone-jar/jar/selenium-server-standalone-2.45.0.jar",
+    "log_path": "tests/nightwatch/logs",
+    "host": "127.0.0.1",
+    "port": 4444,
+    "cli_args": {
+      "webdriver.chrome.driver": "${npm_config_prefix}/lib/node_modules/starrynight/node_modules/chromedriver/bin/chromedriver"
+    }
+  },
+  "test_settings": {
+    "default": {
+      "launch_url": "http://localhost:5000",
+      "selenium_host": "127.0.0.1",
+      "selenium_port": 4444,
+      "pathname": "/wd/hub",
+      "silent": true,
+      "disable_colors": false,
+      "firefox_profile": false,
+      "ie_driver": "",
+      "screenshots": {
+        "enabled": false,
+        "path": "./tests/nightwatch/screenshots"
+      },
+      "desiredCapabilities": {
+        "browserName": "chrome",
+        "javascriptEnabled": true,
+        "acceptSslCerts": true,
+        "loggingPrefs": {
+          "browser": "ALL"
+        }
+      },
+      "exclude": "./tests/nightwatch/unittests/*"
+    },
+    "phantomjs": {
+      "desiredCapabilities": {
+        "browserName": "phantomjs",
+        "javascriptEnabled": true,
+        "databaseEnabled": false,
+        "locationContextEnabled": false,
+        "applicationCacheEnabled": false,
+        "browserConnectionEnabled": false,
+        "webStorageEnabled": false,
+        "acceptSslCerts": true,
+        "rotatable": false,
+        "nativeEvents": false,
+        "phantomjs.binary.path": "${npm_config_prefix}/lib/node_modules/starrynight/node_modules/phantomjs/bin/phantomjs"
+      }
+    },
+    "travis": {
+      "launch_url": "http://localhost:3000",
+      "selenium_host": "127.0.0.1",
+      "selenium_port": 4444,
+      "pathname": "/wd/hub",
+      "silent": true,
+      "disable_colors": false,
+      "firefox_profile": false,
+      "screenshots": {
+        "enabled": false,
+        "path": "./tests/nightwatch/screenshots"
+      },
+      "desiredCapabilities": {
+        "browserName": "firefox",
+        "javascriptEnabled": true,
+        "databaseEnabled": true,
+        "locationContextEnabled": true,
+        "applicationCacheEnabled": true,
+        "browserConnectionEnabled": true,
+        "webStorageEnabled": true,
+        "acceptSslCerts": true,
+        "rotatable": true,
+        "nativeEvents": true
+      }
+    },
+    "travischrome": {
+      "launch_url": "http://localhost:3000",
+      "selenium_host": "127.0.0.1",
+      "selenium_port": 4444,
+      "pathname": "/wd/hub",
+      "silent": true,
+      "disable_colors": false,
+      "firefox_profile": false,
+      "screenshots": {
+        "enabled": false,
+        "path": "./tests/nightwatch/screenshots"
+      },
+      "desiredCapabilities": {
+        "browserName": "chrome",
+        "javascriptEnabled": true,
+        "databaseEnabled": true,
+        "locationContextEnabled": true,
+        "applicationCacheEnabled": true,
+        "browserConnectionEnabled": true,
+        "webStorageEnabled": true,
+        "acceptSslCerts": true,
+        "rotatable": true,
+        "nativeEvents": true,
+        "chromeOptions": {
+          "args": [
+            "--no-sandbox"
+          ]
+        }
+      }
+    },
+    "unittests": {
+      "selenium": {
+        "start_process": false,
+        "start_session": false
+      },
+      "filter": "./tests/nightwatch/unittests/*",
+      "exclude": ""
+    }
+  }
+}

PETSUVMeasurements/.meteor/packages

@@ -0,0 +1,74 @@
+# Meteor packages used by this project, one per line.
+# Check this file (and the other files in this directory) into your repository.
+#
+# 'meteor add' and 'meteor remove' will edit this file for you,
+# but you can also edit it by hand.
+
+npm-bcrypt@0.9.1
+
+meteor-base@1.0.4             # Packages every Meteor app needs to have
+mobile-experience@1.0.4       # Packages for a great mobile UX
+mongo@1.1.12                  # The database Meteor supports right now
+blaze-html-templates@1.0.4    # Compile .html files into Meteor Blaze views
+session@1.1.6                 # Client-side reactive dictionary for your app
+jquery@1.11.9                 # Helpful client-side library
+tracker@1.1.0                 # Meteor's client-side reactive programming library
+
+es5-shim@4.6.14               # ECMAScript 5 compatibility for older browsers.
+ecmascript@0.5.8              # Enable ECMAScript2015+ syntax in app code
+
+insecure
+
+clinical:router
+clinical:extended-api
+clinical:active-entry
+clinical:error-pages
+clinical:theming
+clinical:fonts
+clinical:hipaa-audit-log
+clinical:hipaa-logger
+
+aldeed:simple-schema          # Third party package to deal with schemas
+
+# OHIF Packages
+design
+ohif:core
+ohif:cornerstone
+ohif:viewerbase
+ohif:study-list
+ohif:dicom-services
+ohif:hanging-protocols
+ohif:user-management
+ohif:petsuv
+
+accounts-base@1.2.11
+accounts-password@1.3.0
+
+ian:accounts-ui-bootstrap-3
+twbs:bootstrap
+http@1.2.9
+arsnebula:reactive-promise
+promise@0.8.4
+stylus@2.513.5
+fortawesome:fontawesome
+random@1.0.10
+reactive-var@1.0.10
+reactive-dict@1.1.8
+practicalmeteor:loglevel
+momentjs:moment
+
+anti:gagarin@=0.4.11
+check@1.2.3
+aldeed:template-extension@4.0.0
+zuuk:stale-session
+gilbertwat:bootstrap3-daterangepicker
+email@1.1.17
+peppelg:bootstrap-3-modal
+simple:reactive-method
+fastclick@1.0.12
+standard-minifier-css@1.2.0
+standard-minifier-js@1.2.0
+johdirr:meteor-git-rev
+u2622:persistent-session
+shell-server
+aldeed:collection2

PETSUVMeasurements/.meteor/platforms

@@ -0,0 +1,2 @@
+server
+browser

PETSUVMeasurements/.meteor/release

@@ -0,0 +1 @@
+METEOR@1.4.1.1

PETSUVMeasurements/.meteor/versions

@@ -0,0 +1,143 @@
+accounts-base@1.2.11
+accounts-password@1.3.0
+aldeed:collection2@2.9.1
+aldeed:collection2-core@1.1.1
+aldeed:schema-deny@1.0.1
+aldeed:schema-index@1.0.1
+aldeed:simple-schema@1.5.3
+aldeed:template-extension@4.0.0
+allow-deny@1.0.5
+amplify@1.0.0
+anti:gagarin@0.4.11
+anti:i18n@0.4.3
+arsnebula:reactive-promise@0.9.1
+autoupdate@1.3.11
+babel-compiler@6.9.1
+babel-runtime@0.1.11
+base64@1.0.9
+binary-heap@1.0.9
+blaze@2.1.8
+blaze-html-templates@1.0.4
+blaze-tools@1.0.9
+boilerplate-generator@1.0.9
+caching-compiler@1.1.7
+caching-html-compiler@1.0.6
+callback-hook@1.0.9
+check@1.2.3
+clinical:active-entry@1.5.16
+clinical:auto-resizing@0.2.0
+clinical:error-pages@0.2.0
+clinical:extended-api@2.2.4
+clinical:fonts@1.1.1
+clinical:hipaa-audit-log@2.4.2
+clinical:hipaa-logger@1.0.1
+clinical:router@2.0.19
+clinical:router-location@2.1.0
+clinical:router-middleware-stack@2.1.2
+clinical:router-url@2.1.0
+clinical:theming@0.4.10
+coffeescript@1.2.4_1
+ddp@1.2.5
+ddp-client@1.3.1
+ddp-common@1.2.6
+ddp-rate-limiter@1.0.5
+ddp-server@1.3.10
+deps@1.0.12
+design@0.0.1
+diff-sequence@1.0.6
+ecmascript@0.5.8
+ecmascript-runtime@0.3.14
+ejson@1.0.12
+email@1.1.17
+es5-shim@4.6.14
+fastclick@1.0.12
+fortawesome:fontawesome@4.5.0
+geojson-utils@1.0.9
+gilbertwat:bootstrap3-daterangepicker@1.3.21_1
+grove:less@0.2.0
+hot-code-push@1.0.4
+html-tools@1.0.10
+htmljs@1.0.10
+http@1.2.9
+ian:accounts-ui-bootstrap-3@1.2.89
+id-map@1.0.8
+insecure@1.0.7
+iron:controller@1.0.12
+iron:core@1.0.11
+iron:dynamic-template@1.0.12
+iron:layout@1.0.12
+johdirr:meteor-git-rev@0.0.4
+jquery@1.11.9
+launch-screen@1.0.12
+livedata@1.0.18
+localstorage@1.0.11
+logging@1.1.15
+mdg:validation-error@0.5.1
+meteor@1.2.17
+meteor-base@1.0.4
+meteor-platform@1.2.6
+minifier-css@1.2.14
+minifier-js@1.2.14
+minimongo@1.0.17
+mobile-experience@1.0.4
+mobile-status-bar@1.0.12
+modules@0.7.6
+modules-runtime@0.7.6
+momentjs:moment@2.14.4
+mongo@1.1.12
+mongo-id@1.0.5
+mrt:moment@2.8.1
+natestrauser:select2@4.0.3
+npm-bcrypt@0.9.1
+npm-mongo@1.5.49
+observe-sequence@1.0.12
+ohif:core@0.0.1
+ohif:cornerstone@0.0.1
+ohif:dicom-services@0.0.1
+ohif:hanging-protocols@0.0.1
+ohif:measurements@0.0.1
+ohif:petsuv@0.0.1
+ohif:study-list@0.0.1
+ohif:user-management@0.0.1
+ohif:viewerbase@0.0.1
+ohif:wadoproxy@0.0.1
+ordered-dict@1.0.8
+peppelg:bootstrap-3-modal@1.0.4
+practicalmeteor:chai@2.1.0_1
+practicalmeteor:loglevel@1.2.0_2
+promise@0.8.4
+raix:eventemitter@0.1.3
+random@1.0.10
+rate-limit@1.0.5
+reactive-dict@1.1.8
+reactive-var@1.0.10
+reload@1.1.10
+retry@1.0.8
+routepolicy@1.0.11
+service-configuration@1.0.10
+session@1.1.6
+sha@1.0.8
+shell-server@0.2.1
+silentcicero:jszip@0.0.4
+simple:reactive-method@1.0.2
+spacebars@1.0.12
+spacebars-compiler@1.0.12
+srp@1.0.9
+standard-app-packages@1.0.9
+standard-minifier-css@1.2.0
+standard-minifier-js@1.2.0
+stylus@2.513.5
+templating@1.2.14
+templating-tools@1.0.4
+tracker@1.1.0
+twbs:bootstrap@3.3.6
+typ:accounts-ldap@1.0.1
+typ:ldapjs@0.7.3
+u2622:persistent-session@0.4.4
+ui@1.0.11
+underscore@1.0.9
+url@1.0.10
+validatejs@0.0.1
+webapp@1.3.11
+webapp-hashing@1.0.9
+zuuk:stale-session@1.0.8

PETSUVMeasurements/activeEntry.js

@@ -0,0 +1,46 @@
+if (Meteor.isClient){
+    ActiveEntry.configure({
+        logo: {
+            url: '/mini-circles.png',
+            displayed: true
+        },
+        signIn: {
+            displayFullName: true,
+            destination: '/worklist'
+        },
+        signUp: {
+            destination: '/worklist'
+        },
+        themeColors: {
+            primary: ""
+        },
+        passwordOptions: {
+            showPasswordStrengthIndicator: false,
+            requireRegexValidation: true,
+            //requireStrongPasswords: false
+            passwordHistoryCount: 6,
+            failedAttemptsLimit: 5
+        }
+
+    });
+}
+
+/*
+if (Meteor.isServer){
+    Accounts.emailTemplates.siteName = 'AwesomeSite';
+    Accounts.emailTemplates.from = 'AwesomeSite Admin <accounts@example.com>';
+    Accounts.emailTemplates.enrollAccount.subject = function(user) {
+        return 'Welcome to Awesome Town, ' + user.profile.name;
+    };
+
+    Accounts.emailTemplates.enrollAccount.text = function(user, url) {
+        return 'You have been selected to participate in building a better future!'
+            + ' To activate your account, simply click the link below:\n\n'
+            + url;
+    };
+
+    Meteor.startup(function() {
+        //process.env.MAIL_URL = 'smtp://sandboxid.mailgun.org:mypassword@smtp.mailgun.org:587';
+    });
+}
+*/

PETSUVMeasurements/client/body.styl

@@ -0,0 +1,2 @@
+body
+  background-color: black

PETSUVMeasurements/client/components/app/app.html

@@ -0,0 +1,40 @@
+<template name="app">
+    <div class="topBar noselect {{#if onStudyList}}studyList{{/if}}">
+        <div class="clearfix p-x-1 p-t-1">
+            <a target='_blank'
+               class="brandSection pull-left"
+               href="http://ohif.org">
+                <svg class="logoImage">
+                    <use xlink:href="/packages/ohif_viewerbase/assets/icons.svg#icon-ohif-logo"></use>
+                </svg>
+                <div class="logoText">
+                    Open Health Imaging Foundation
+                </div>
+            </a>
+            {{ #if studyListToggleText }}
+            <a class="btn studyListLinkSection pull-left m-x-1 p-x-2 p-y-0 js-toggle-studyList">
+                {{studyListToggleText}}
+            </a>
+            {{ /if }}
+            <div class="userAccountSection pull-right">
+                {{>userAccountMenu}}
+            </div>
+        </div>
+    </div>
+    {{ >timeoutCountdownDialog }}
+    <div id="studylistTabs" class="tab-content">
+        <div class="tab-pane active" id="studylistTab">
+            <div class="studylistContainer">
+                {{> studylistResult }}
+            </div>
+        </div>
+        <div class="tab-pane" id="viewerTab">
+        </div>
+    </div>
+    {{ >associationModal }}
+    {{ >serverInformationModal }}
+    {{ >lastLoginModal }}
+    {{ >studyContextMenu }}
+    {{ >progressDialog }}
+    {{ >viewSeriesDetailsModal }}
+</template>

PETSUVMeasurements/client/components/app/app.js

@@ -0,0 +1,46 @@
+const studylistContentId = 'studylistTab';
+const viewerContentId = 'viewerTab';
+
+// Define the ViewerData global object
+// If there is currently any Session data for this object,
+// use this to repopulate the variable
+Template.app.onCreated(() => {
+    ViewerData = Session.get('ViewerData') || {};
+});
+
+Template.app.events({
+    'click .js-toggle-studyList'() {
+        const contentId = Session.get('activeContentId');
+
+        if (contentId !== studylistContentId) {
+            switchToTab(studylistContentId);
+        } else {
+            switchToTab(viewerContentId);
+        }
+    }
+});
+
+Template.app.helpers({
+    studyListToggleText() {
+        const contentId = Session.get('activeContentId');
+        
+        // If the Viewer has not been opened yet, 'Back to viewer' should
+        // not be displayed
+        const viewerContentExists = !!Object.keys(ViewerData).length;
+        if (!viewerContentExists) {
+            return;
+        }
+
+        if (contentId === studylistContentId) {
+            return 'Back to viewer';
+        } else if (contentId === viewerContentId) {
+            return 'Study list';
+        }
+    },
+
+    onStudyList() {
+        return (Session.get('activeContentId') === 'studylistTab');
+    }
+});
+
+Session.set('defaultSignInMessage', 'Tumor tracking in your browser.');

PETSUVMeasurements/client/components/app/app.styl

@@ -0,0 +1,79 @@
+@import "{design}/app"
+
+$expandedHeight = 160px
+
+.logoImage
+  display: inline-block
+  height: 100%
+  float: left
+
+.topBar
+  height: $topBarHeight
+  theme('color', '$textPrimaryColor')
+  theme('background-color', '$primaryBackgroundColor')
+  transition(all 0.5s ease)
+
+  .brandSection
+    height: 30px
+    display: inline-block
+    text-decoration: none
+
+    .logoImage
+      margin: 0 8px
+      width: 30px
+
+    .logoText
+      display: inline-block
+      font-family: $logoFontFamily
+      font-weight: $logoFontWeight
+      theme('color', '$textPrimaryColor')
+      line-height: 30px
+
+  .studyListLinkSection
+    theme('border-left', '%s solid $uiBorderColor' % $uiBorderThickness)
+
+  .btn
+    theme('color', '$textSecondaryColor')
+    cursor: pointer
+    font-size: 13px
+    font-weight: 500
+    line-height: 26px
+    margin-top: 3px
+
+    &:hover
+      theme('color', '$hoverColor')
+
+    &:active
+      theme('color', '$activeColor')
+
+  &.studyList
+    background-color: rgba(21, 25, 30, 0.7)
+    height: $expandedHeight
+
+    .brandSection
+      height: 100%
+      width: 80%
+      padding-left: 50px
+      line-height: $expandedHeight
+
+      .logoImage
+        width: 50px
+        margin: 0 20px
+
+      .logoText
+        font-size: 30px
+
+    .studyListLinkSection
+      position: absolute
+      border: none
+      top: 5px
+      left: 5px
+
+#studylistTabs
+  height: "calc(100% - %s)" % $topBarHeight
+
+  .tab-pane
+    .viewerContainer
+      .loadingTextDiv
+        theme('color', '$textSecondaryColor')
+        font-size: 30px

PETSUVMeasurements/client/components/toolbarSection/toolbarSection.html

@@ -0,0 +1,33 @@
+<template name="toolbarSection">
+    <div class="toolbarSection noselect p-x-2">
+        <div class="clearfix">
+            <div class="pull-left m-t-1">
+                {{>roundedButtonGroup leftSidebarToggleButtonData}}
+            </div>
+
+            {{>toolbarSectionTools toolbarButtons=toolbarButtons extraToolbarButtons=extraToolbarButtons}}
+
+            {{#if splitView}}
+                {{>studySeriesQuickSwitch (clone this side="right" viewportIndex=1)}}
+                {{>studySeriesQuickSwitch (clone this side="left" viewportIndex=0)}}
+            {{else}}
+                {{>studySeriesQuickSwitch (clone this side="middle" viewportIndex=0)}}
+            {{/if}}
+
+            <div class="toolbarSectionEntry pull-right rm-l-1 p-x-1">
+                {{>caseProgress}}
+            </div>
+            <div class="pull-right m-t-1 rm-x-1">
+                {{>roundedButtonGroup rightSidebarToggleButtonData}}
+            </div>
+            <div id="toggleHUD" class="toolbarSectionButton pull-right rp-x-1 m-t-1 rm-r-3 {{#if session 'measurementTableHudOpen'}}active{{/if}}">
+                <div class="svgContainer">
+                    <svg>
+                        <use xlink:href="/packages/ohif_viewerbase/assets/icons.svg#icon-hud"></use>
+                    </svg>
+                </div>
+                <div class="buttonLabel">HUD</div>
+            </div>
+        </div>
+    </div>
+</template>

PETSUVMeasurements/client/components/toolbarSection/toolbarSection.js

@@ -0,0 +1,143 @@
+import { OHIF } from 'meteor/ohif:core';
+
+Template.toolbarSection.helpers({
+    // Returns true if the view shall be split in two viewports
+    splitView() {
+        // Run this computation every time the viewports are updated
+        Session.get('LayoutManagerUpdated');
+
+        // Stops here if layout manager is not defined yet
+        if (!window.layoutManager) {
+            return;
+        }
+
+        return window.layoutManager.viewportData.length > 1;
+    },
+
+    leftSidebarToggleButtonData() {
+        const instance = Template.instance();
+        return {
+            toggleable: true,
+            key: 'leftSidebar',
+            value: instance.data.state,
+            options: [{
+                value: 'studies',
+                svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-studies',
+                svgWidth: 15,
+                svgHeight: 13,
+                bottomLabel: 'Studies'
+            }]
+        };
+    },
+
+    rightSidebarToggleButtonData() {
+        const instance = Template.instance();
+        return {
+            toggleable: true,
+            key: 'rightSidebar',
+            value: instance.data.state,
+            options: [{
+                value: 'measurements',
+                svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-measurements-lesions',
+                svgWidth: 18,
+                svgHeight: 10,
+                bottomLabel: 'Measurements'
+            }]
+        };
+    },
+
+    toolbarButtons() {
+        // Check if the measure tools shall be disabled
+        const isToolDisabled = false; //!Template.instance().data.timepointApi;
+        
+        const buttonData = [];
+
+        buttonData.push({
+            id: 'zoom',
+            title: 'Zoom',
+            classes: 'imageViewerTool',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-zoom'
+        });
+
+        buttonData.push({
+            id: 'wwwc',
+            title: 'Levels',
+            classes: 'imageViewerTool',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-levels'
+        });
+
+        buttonData.push({
+            id: 'pan',
+            title: 'Pan',
+            classes: 'imageViewerTool',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-pan'
+        });
+
+        buttonData.push({
+            id: 'ellipticalRoi',
+            title: 'Ellipse',
+            classes: 'imageViewerTool',
+            iconClasses: 'fa fa-circle-o'
+        });
+
+        return buttonData;
+    },
+
+    extraToolbarButtons() {
+        // Check if the measure tools shall be disabled
+        const isToolDisabled = false; //!Template.instance().data.timepointApi.currentTimepointId;
+        const buttonData = [];
+
+        // TODO: Get real icons for CR / UN / EX
+        buttonData.push({
+            id: 'crTool',
+            title: 'CR Tool',
+            classes: 'imageViewerTool toolbarSectionButton',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-temp',
+            disabled: isToolDisabled
+        });
+
+        buttonData.push({
+            id: 'unTool',
+            title: 'UN Tool',
+            classes: 'imageViewerTool toolbarSectionButton',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-temp',
+            disabled: isToolDisabled
+        });
+
+        buttonData.push({
+            id: 'exTool',
+            title: 'EX Tool',
+            classes: 'imageViewerTool toolbarSectionButton',
+            svgLink: '/packages/ohif_viewerbase/assets/icons.svg#icon-tools-measure-temp',
+            disabled: isToolDisabled
+        });
+
+        return buttonData;
+    }
+});
+
+Template.toolbarSection.events({
+    'click #toggleHUD'() {
+        const state = Session.get('measurementTableHudOpen');
+        Session.set('measurementTableHudOpen', !state);
+    }
+});
+
+Template.toolbarSection.onRendered(function() {
+    // Set disabled/enabled tool buttons that are set in toolManager
+    const states = toolManager.getToolDefaultStates();
+    const disabledToolButtons = states.disabledToolButtons;
+    const allToolbarButtons = $('#toolbar').find('button');
+    if (disabledToolButtons && disabledToolButtons.length > 0) {
+        for (var i = 0; i < allToolbarButtons.length; i++) {
+            const toolbarButton = allToolbarButtons[i];
+            $(toolbarButton).prop('disabled', false);
+
+            const index = disabledToolButtons.indexOf($(toolbarButton).attr('id'));
+            if (index !== -1) {
+                $(toolbarButton).prop('disabled', true);
+            }
+        }
+    }
+});

PETSUVMeasurements/client/components/toolbarSection/toolbarSection.styl

@@ -0,0 +1,24 @@
+@import "{design}/app"
+
+.toolbarSection
+  theme('border-bottom', '%s solid $uiBorderColor' % $uiBorderThickness)
+  flex: 0 0 auto
+  height: $toolbarHeight
+  overflow: hidden
+  padding-top: 6px
+  position: relative
+  transition(height 300ms ease)
+  width: 100%
+
+  &.expanded
+    height: $toolbarHeight + $toolbarDrawerHeight
+
+  .toolbarSectionEntry
+    theme('color', '$defaultColor')
+    cursor: pointer
+    display: inline-block
+    theme('fill', '$defaultColor')
+    margin-top: 3px
+    min-width: 30px
+    theme('stroke', '$defaultColor')
+    text-align: center

PETSUVMeasurements/client/components/viewer/viewer.html

@@ -2,15 +2,11 @@
     {{#if Template.subscriptionsReady}}
         <div class="viewerDialogs">
             {{>confirmDeleteDialog}}
-            {{>lesionLocationDialog}}
+            {{>measurementTableHUD (clone this)}}
-            {{>nonTargetLesionDialog}}
-            {{>nonTargetResponseDialog}}
-            {{>lesionTableHUD (clone this)}}
-            {{! >conformanceCheckFeedback}}
         </div>
         <div id="viewer">
             {{>toolbarSection (clone this)}}
-            {{>flexboxLayout (clone this)}}
+            {{>viewerSection (clone this)}}
         </div>
     {{else}}
         {{>loadingText}}

PETSUVMeasurements/client/components/viewer/viewer.js

@@ -0,0 +1,68 @@
+import { OHIF } from 'meteor/ohif:core';
+import { MeasurementsConfiguration } from 'meteor/ohif:measurements/both/configuration/measurements';
+import { MeasurementHandlers } from 'meteor/ohif:measurements/client/lib/MeasurementHandlers';
+
+Session.set('MeasurementsReady', false);
+
+Template.viewer.onCreated(() => {
+    const MeasurementApi = MeasurementsConfiguration.getMeasurementsApi();
+
+    OHIF.viewer = OHIF.viewer || {};
+
+    const instance = Template.instance();
+
+    instance.data.state = new ReactiveDict();
+    instance.data.state.set('leftSidebar', Session.get('leftSidebar'));
+    instance.data.state.set('rightSidebar', Session.get('rightSidebar'));
+
+    const contentId = instance.data.contentId;
+
+    if (ViewerData[contentId].loadedSeriesData) {
+        log.info('Reloading previous loadedSeriesData');
+        OHIF.viewer.loadedSeriesData = ViewerData[contentId].loadedSeriesData;
+
+    } else {
+        log.info('Setting default ViewerData');
+        OHIF.viewer.loadedSeriesData = {};
+        ViewerData[contentId].loadedSeriesData = {};
+        Session.set('ViewerData', ViewerData);
+    }
+
+    Session.set('activeViewport', ViewerData[contentId].activeViewport || false);
+
+    // Update the ViewerStudies collection with the loaded studies
+    ViewerStudies.remove({});
+
+    instance.data.studies.forEach(study => {
+        study.selected = true;
+        study.displaySets = createStacks(study);
+        ViewerStudies.insert(study);
+    });
+
+    instance.data.measurementApi = new MeasurementApi();
+    const measurementsPromise = instance.data.measurementApi.retrieveMeasurements();
+    measurementsPromise.then(() => {
+        Session.set('MeasurementsReady', true);
+
+        instance.data.measurementApi.syncMeasurementsAndToolData();
+    })
+});
+
+Template.viewer.helpers({
+    dataSourcesReady() {
+        // TODO: Find a better way to do this
+        return Session.get('MeasurementsReady');
+    }
+})
+
+Template.viewer.events({
+    'CornerstoneToolsMeasurementAdded .imageViewerViewport'(event, instance, eventData) {
+        MeasurementHandlers.onAdded(event, instance, eventData);
+    },
+    'CornerstoneToolsMeasurementModified .imageViewerViewport'(event, instance, eventData) {
+        MeasurementHandlers.onModified(event, instance, eventData);
+    },
+    'CornerstoneToolsMeasurementRemoved .imageViewerViewport'(event, instance, eventData) {
+        MeasurementHandlers.onRemoved(event, instance, eventData);
+    }
+});

PETSUVMeasurements/client/components/viewer/viewer.styl

@@ -0,0 +1,22 @@
+@import "{design}/app"
+
+#viewer
+  background-color: black
+  height: 100%
+  width: 100%
+
+#imageViewerViewports
+  .viewportContainer
+    border: none !important
+    outline: 0 !important // Prevent blue outline in Chrome
+
+    &:hover
+    &.active
+    &:hover.active
+      border: none !important
+      outline: 0 !important // Prevent blue outline in Chrome
+
+    &:not(:last-child)
+    .removable
+      .imageViewerViewport
+        theme('border-right', '%s solid $uiBorderColor' % $uiBorderThickness)

PETSUVMeasurements/client/components/viewerSection/viewerSection.html

@@ -0,0 +1,13 @@
+<template name="viewerSection">
+    <div class="viewerSection">
+        <div class="sidebarMenu sidebar-left {{#if leftSidebarOpen}}sidebar-open{{/if}}">
+            {{>studyTimepointBrowser (clone this)}}
+        </div>
+        <div class="mainContent {{#if leftSidebarOpen}}sidebar-left-open{{/if}} {{#if rightSidebarOpen}}sidebar-right-open{{/if}}">
+            {{>viewerMain (clone this)}}
+        </div>
+        <div class="sidebarMenu sidebar-right {{#if rightSidebarOpen}}sidebar-open{{/if}}">
+            {{>measurementTable (clone this)}}
+        </div>
+    </div>
+</template>

PETSUVMeasurements/client/components/viewerSection/viewerSection.js

@@ -0,0 +1,19 @@
+Template.viewerSection.events({
+    'transitionend .sidebarMenu'(event) {
+        if (!event.target.classList.contains('sidebarMenu')) {
+            return;
+        }
+
+        handleResize();
+    }
+});
+
+Template.viewerSection.helpers({
+    leftSidebarOpen() {
+        return Template.instance().data.state.get('leftSidebar');
+    },
+
+    rightSidebarOpen() {
+        return Template.instance().data.state.get('rightSidebar');
+    }
+});

PETSUVMeasurements/client/components/viewerSection/viewerSection.styl

@@ -0,0 +1,78 @@
+@import "{design}/app"
+
+.viewerSection
+  display: flex
+  flex: 1
+  flex-flow: row nowrap
+  align-items: stretch
+  height: calc(100% - 78px);
+  width: 100%
+
+  .sidebarMenu
+    height: 100%
+    // required transformation to make inner fixed elements relative to this one
+    transform(scale(1))
+    transition($sidebarTransition)
+
+    .sidebar-option
+      height: 100%
+      position: fixed
+      transform(translateX(100%))
+      transition($sidebarTransition)
+      width: 100%
+
+      &.active
+        transform(translateX(0%))
+
+  .sidebar-left
+    theme('border-right', '%s solid $uiBorderColor' % $uiBorderThickness)
+    flex: 1
+    margin-left: - $studiesSidebarMenuWidth
+    max-width: $studiesSidebarMenuWidth
+    order: 1
+
+    &.sidebar-open
+      margin-left: 0
+
+  .mainContent
+    flex: 1
+    order: 2
+    width: 100%
+    height: 100%
+    overflow: hidden
+    transition($sidebarTransition)
+
+  .sidebar-right
+    flex: 1
+    margin-left: -12px
+    margin-right: - $lesionsSidebarMenuWidth
+    max-width: $lesionsSidebarMenuWidth
+    order: 3
+    padding-left: 6px
+    position: relative
+
+    &[data-timepoints="3"]
+      margin-right: - ($lesionsSidebarMenuWidth + 135.5px)
+      max-width: $lesionsSidebarMenuWidth + 135.5px
+
+    &[data-timepoints="4"]
+      margin-right: - ($lesionsSidebarMenuWidth + 270px)
+      max-width: $lesionsSidebarMenuWidth + 270px
+
+    &:before
+      theme('background-color', '$uiBorderColor')
+      content: ''
+      display: block
+      height: 100%
+      left: 5px
+      position: absolute
+      top: 0
+      width: $uiBorderThickness
+
+    &.sidebar-open
+      margin-right: 0
+
+  .studiesListedChanger
+    theme('border-bottom', '%s solid $uiBorderColor' % $uiBorderThickness)
+    padding: 20px 10px
+    text-align: center

PETSUVMeasurements/client/head.html

@@ -0,0 +1,20 @@
+<head>
+    <meta charset="utf-8">
+    <title>Lesion Tracker</title>
+    <meta name="description" content="Prototype viewer application for oncology">
+    <!-- Prevents page zooming -->
+    <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1, user-scalable=no">
+
+    <link rel="shortcut icon" type="image/png" href="images/logo.png" sizes="16x16 32x32 64x64">
+    <!--Best display for mobile devices-->
+    <meta http-equiv="cleartype" content="on">
+    <meta name="MobileOptimized" content="320">
+    <meta name="HandheldFriendly" content="True">
+    <meta name="apple-mobile-web-app-capable" content="yes">
+
+    <!-- Make SVG work on IE -->
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+
+    <link href='http://fonts.googleapis.com/css?family=Roboto:400,100,100italic,300,300italic,400italic,500,500italic,700,700italic,900,900italic&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
+    <link href='http://fonts.googleapis.com/css?family=Sanchez:400,700&subset=latin,latin-ext' rel='stylesheet' type='text/css'>
+</head>

PETSUVMeasurements/client/lesionTrackerHangingProtocol.js

@@ -0,0 +1,167 @@
+// Define Baseline protocol
+var proto = new HP.Protocol('LT_Baseline');
+proto.locked = true;
+
+var studyDescription = new HP.ProtocolMatchingRule();
+studyDescription.required = true;
+studyDescription.attribute = 'studyDescription';
+studyDescription.constraint = {
+    contains: {
+        value: 'CT'
+    }
+};
+
+var isBaseline = new HP.ProtocolMatchingRule();
+isBaseline.required = true;
+isBaseline.attribute = 'timepointType';
+isBaseline.constraint = {
+    equals: {
+        value: 'baseline'
+    }
+};
+
+proto.addProtocolMatchingRule(studyDescription);
+proto.addProtocolMatchingRule(isBaseline);
+
+var oneByOne = new HP.ViewportStructure('grid', {
+    rows: 1,
+    columns: 1
+});
+
+// Stage 1
+var single = new HP.Viewport();
+
+var baseline = new HP.StudyMatchingRule(true);
+baseline.required = true;
+baseline.attribute = 'timepointType';
+baseline.constraint = {
+    equals: {
+        value: 'baseline'
+    }
+};
+
+var body = new HP.SeriesMatchingRule();
+body.attribute = 'seriesDescription';
+body.weight = 5;
+body.constraint = {
+    contains: {
+        value: 'Body'
+    }
+};
+
+var chest = new HP.SeriesMatchingRule();
+chest.attribute = 'seriesDescription';
+chest.constraint = {
+    contains: {
+        value: 'CHEST'
+    }
+};
+
+single.studyMatchingRules.push(baseline);
+single.seriesMatchingRules.push(body);
+single.seriesMatchingRules.push(chest);
+
+var first = new HP.Stage(oneByOne, 'oneByOne');
+first.viewports.push(single);
+
+proto.addStage(first);
+
+HP.lesionTrackerBaselineProtocol = proto;
+HP.lesionTrackerBaselineProtocol.id = 'lesionTrackerBaselineProtocol';
+
+
+// Define Followup Protocol
+var proto = new HP.Protocol('LT_BaselineFollowup');
+proto.locked = true;
+
+var studyDescription = new HP.ProtocolMatchingRule();
+studyDescription.required = true;
+studyDescription.attribute = 'studyDescription';
+studyDescription.constraint = {
+    contains: {
+        value: 'CT'
+    }
+};
+
+var isFollowup = new HP.ProtocolMatchingRule();
+isFollowup.required = true;
+isFollowup.attribute = 'timepointType';
+isFollowup.constraint = {
+    equals: {
+        value: 'followup'
+    }
+};
+
+proto.addProtocolMatchingRule(studyDescription);
+proto.addProtocolMatchingRule(isFollowup);
+
+var oneByTwo = new HP.ViewportStructure('grid', {
+    rows: 1,
+    columns: 2
+});
+
+// Stage 1
+var left = new HP.Viewport();
+var right = new HP.Viewport();
+
+var baseline = new HP.StudyMatchingRule(true);
+baseline.required = true;
+baseline.attribute = 'timepointType';
+baseline.constraint = {
+    equals: {
+        value: 'baseline'
+    }
+};
+
+var followup = new HP.StudyMatchingRule();
+followup.required = true;
+followup.attribute = 'timepointType';
+followup.constraint = {
+    equals: {
+        value: 'followup'
+    }
+};
+
+var body = new HP.SeriesMatchingRule();
+body.attribute = 'seriesDescription';
+body.weight = 5;
+body.constraint = {
+    contains: {
+        value: 'Body'
+    }
+};
+
+var chest = new HP.SeriesMatchingRule();
+chest.attribute = 'seriesDescription';
+chest.constraint = {
+    contains: {
+        value: 'CHEST'
+    }
+};
+
+left.studyMatchingRules.push(baseline);
+//left.seriesMatchingRules.push(body);
+//left.seriesMatchingRules.push(chest);
+
+right.studyMatchingRules.push(followup);
+//right.seriesMatchingRules.push(body);
+//right.seriesMatchingRules.push(chest);
+
+var first = new HP.Stage(oneByTwo, 'oneByTwo');
+first.viewports.push(left);
+first.viewports.push(right);
+
+proto.addStage(first);
+
+HP.lesionTrackerFollowupProtocol = proto;
+HP.lesionTrackerFollowupProtocol.id = 'lesionTrackerFollowupProtocol';
+
+Meteor.call('removeHangingProtocolByID', HP.lesionTrackerBaselineProtocol.id, function() {
+    HangingProtocols.insert(HP.lesionTrackerBaselineProtocol);
+});
+
+Meteor.call('removeHangingProtocolByID', HP.lesionTrackerFollowupProtocol.id, function() {
+    HangingProtocols.insert(HP.lesionTrackerFollowupProtocol);
+});
+
+HangingProtocols.insert(HP.defaultProtocol);

PETSUVMeasurements/client/log.js

@@ -0,0 +1,3 @@
+// Create application logger using loglevel
+// https://atmospherejs.com/spacejamio/loglevel
+log = loglevel.createAppLogger('PETSUVMeasurements', defaultLevel = 'info');

PETSUVMeasurements/client/routes.js

@@ -0,0 +1,55 @@
+Session.setDefault('ViewerData', {});
+
+// verifyEmail controls whether emailVerification template will be rendered or not
+var verifyEmail = Meteor.settings && Meteor.settings.public && Meteor.settings.public.verifyEmail || false;
+
+Router.configure({
+    layoutTemplate: 'layout',
+    loadingTemplate: 'layout'
+});
+
+Router.onBeforeAction('loading');
+
+var data = {
+    additionalTemplates: []
+};
+
+var routerOptions = {
+    data: data
+};
+
+Router.route('/', function() {
+    // Check user is logged in
+    if (Meteor.user() && Meteor.userId()) {
+        if (verifyEmail && Meteor.user().emails && !Meteor.user().emails[0].verified) {
+            this.render('emailVerification', routerOptions);
+        } else {
+            Session.set('activeContentId', 'studylistTab');
+            this.render('app', routerOptions);
+        }
+
+    } else {
+        this.render('entrySignIn', routerOptions);
+    }
+});
+
+Router.route('/viewer/timepoints/:_id', {
+    layoutTemplate: 'layout',
+    name: 'viewer',
+    onBeforeAction: function() {
+        var timepointId = this.params._id;
+
+        this.render('app', routerOptions);
+        openNewTabWithTimepoint(timepointId);
+    }
+});
+
+Router.onBeforeAction(function() {
+    if (!Meteor.userId() && !Meteor.loggingIn()) {
+        this.render('entrySignIn');
+    } else {
+        this.next();
+    }
+}, {
+    except: ['entrySignIn', 'entrySignUp', 'forgotPassword', 'resetPassword']
+});

PETSUVMeasurements/server/dropAllCollections.js

@@ -0,0 +1,12 @@
+// Temporary fix to drop all Collections on server restart
+// http://stackoverflow.com/questions/23891631/meteor-how-can-i-drop-all-mongo-collections-and-clear-all-data-on-startup
+Meteor.startup(function() {
+    console.warn('Dropping all Collections!');
+    for (var property in global) {
+        var object = global[property];
+        if (object instanceof Meteor.Collection) {
+        	console.warn('Dropping: ' + object._debugName);
+            object.remove({});
+        }
+    }
+});

PETSUVMeasurements/server/email.js

@@ -0,0 +1,50 @@
+Meteor.startup(function () {
+
+    // Mail server settings
+    var username = Meteor.settings && Meteor.settings.mailServerSettings && Meteor.settings.mailServerSettings.username || null;
+    var password = Meteor.settings && Meteor.settings.mailServerSettings && Meteor.settings.mailServerSettings.password || null;
+    var server = Meteor.settings && Meteor.settings.mailServerSettings && Meteor.settings.mailServerSettings.server || null;
+    var port = Meteor.settings && Meteor.settings.mailServerSettings && Meteor.settings.mailServerSettings.port || null;
+    var verifyEmail = Meteor.settings && Meteor.settings.public && Meteor.settings.public.verifyEmail || false;
+    var siteName = Meteor.settings && Meteor.settings.public && Meteor.settings.public.siteName || "Lesion Tracker";
+
+    if (username && password && server && port) {
+        Accounts.emailTemplates.siteName = siteName;
+        Accounts.emailTemplates.from = siteName+' Admin <'+username+'>';
+
+        process.env.MAIL_URL = 'smtp://' +
+            encodeURIComponent(username) + ':' +
+            encodeURIComponent(password) + '@' +
+            encodeURIComponent(server) + ':' + port;
+
+        // Subject line of the email.
+        Accounts.emailTemplates.verifyEmail.subject = function(user) {
+            return 'Confirm Your Email Address for '+siteName;
+        };
+
+        // Email text
+        Accounts.emailTemplates.verifyEmail.text = function(user, url) {
+            return 'Thank you for registering.  Please click on the following link to verify your email address: \r\n' + url;
+        };
+
+        // Reset password mail
+        Accounts.emailTemplates.resetPassword.subject = function() {
+          return 'Reset your '+siteName+' password'
+        };
+
+        Accounts.urls.resetPassword = function(token) {
+            return Meteor.absoluteUrl('resetPassword/' + token);
+        };
+
+        Accounts.emailTemplates.resetPassword.text = function(user, url) {
+            return "Hello " + user.profile.fullName + ",\n\n" +
+                "Click the following link to set your new password:\n" +
+                url + "\n\n";
+        };
+
+        // Send email when account is created
+        Accounts.config({
+            sendVerificationEmail: verifyEmail
+        });
+    }
+});

Packages/dicomweb/package.js

@@ -1,21 +0,0 @@
-Package.describe({
-    name: 'dicomweb',
-    summary: 'DICOM Web Helper Functions',
-    version: '0.0.1'
-});
-
-Package.onUse(function(api) {
-    api.use('http');
-
-    // DICOMWeb API functions
-    api.addFiles('server/namespace.js', 'server');
-    api.addFiles('server/getAttribute.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');
-    api.addFiles('server/getModalities.js', 'server');
-
-    api.export('DICOMWeb', ['client', 'server']);
-});
-

Packages/dimseservice/package.js

@@ -1,24 +0,0 @@
-Package.describe({
-    name: 'dimseservice',
-    summary: 'DICOM DIMSE C-Service',
-    version: '0.0.1'
-});
-
-Package.onUse(function(api) {
-    api.versionsFrom('1.4');
-
-    api.use('ecmascript');
-    api.addFiles('server/require.js', 'server');
-    api.addFiles('server/constants.js', 'server');
-    api.addFiles('server/elements_data.js', 'server');
-    api.addFiles('server/Field.js', 'server');
-    api.addFiles('server/RWStream.js', 'server');
-    api.addFiles('server/Data.js', 'server');
-    api.addFiles('server/Message.js', 'server');
-    api.addFiles('server/PDU.js', 'server');
-    api.addFiles('server/CSocket.js', 'server');
-    api.addFiles('server/Connection.js', 'server');
-    api.addFiles('server/DIMSE.js', 'server');
-
-    api.export('DIMSE', 'server');
-});

Packages/lesiontracker/both/collections.js

@@ -1,16 +0,0 @@
-import { Mongo } from 'meteor/mongo';
-
-Timepoints = new Mongo.Collection('timepoints');
-Studies = new Mongo.Collection('studies');
-Measurements = new Mongo.Collection('measurements');
-
-// ImageMeasurements describe temporary measurements that aren't
-// specifically listed in the Lesion Table
-ImageMeasurements = new Mongo.Collection('imageMeasurements');
-
-// Additional Findings stores details from the Additional Findings
-// panel, and represents items such as data quality,
-AdditionalFindings = new Mongo.Collection('additionalFindings');
-
-WorklistSubscriptions = ['studies', 'timepoints'];
-Reviewers = new Mongo.Collection('reviewers');

Packages/lesiontracker/both/schema/additionalFindings.js

@@ -1,54 +0,0 @@
-import { SimpleSchema } from 'meteor/aldeed:simple-schema';
-
-export const schema = new SimpleSchema({
-    measurableDisease: {
-        type: String,
-        label: 'Measurable disease',
-        allowedValues: ['Present', 'Absent'],
-        defaultValue: 'Absent',
-        optional: true
-    },
-    // TODO: Add check so that the value cannot be None & something other region
-    regionsOfMetastaticDisease: {
-        type: [String],
-        label: 'Regions of metastatic disease',
-        allowedValues: ['None', 'Lymph Node'],
-        defaultValue: ['None'],
-        optional: true
-    },
-    tracerRelatedToMetastaticDisease: {
-        type: String,
-        label: 'Tracer related to metastatic disease?',
-        allowedValues: ['Yes', 'No'],
-        defaultValue: 'Yes',
-        optional: true
-    },
-    numberOfBoneLesions: {
-        type: String,
-        label: 'Number of bone lesions',
-        allowedValues: ['0', '1-2', '2-4', '>5'],
-        defaultValue: '0',
-        optional: true
-    },
-    acceptableImageQuality: {
-        type: String,
-        label: 'Acceptable image quality',
-        allowedValues: ['Yes', 'No'],
-        defaultValue: 'Yes',
-        optional: true
-    },
-    adequateAnatomicalCoverage: {
-        type: String,
-        label: 'Adequate anatomical coverage',
-        allowedValues: ['Yes', 'No'],
-        defaultValue: 'Yes',
-        optional: true
-    },
-    presenceOfContrast: {
-        type: String,
-        label: 'Presence of contrast',
-        allowedValues: ['Yes', 'No'],
-        defaultValue: 'Yes',
-        optional: true
-    }
-});

Packages/lesiontracker/client/api/measurement.js

@@ -1,102 +0,0 @@
-const hasValueAtTimepoint = timepointId => {
-    return measurement => {
-        if (measurement.timepoints[timepointId]) {
-            return true;
-        }
-    };
-};
-
-const hasNoValueAtTimepoint = timepointId => {
-    return measurement => {
-        if (measurement.timepoints[timepointId] === undefined) {
-            return true;
-        }
-    };
-};
-
-export const MeasurementApi = {
-    sortOptions: {
-        sort: {
-            lesionNumberAbsolute: 1
-        }
-    },
-
-    // Return all Measurements
-    all(withPriors=false) {
-        let data = Measurements.find({}, this.sortOptions).fetch();
-
-        // If we don't have a prior for this Timepoint,
-        // this filter, we should just return all of the
-        // available Non-Targets measurements
-        if (this.priorTimepointId && withPriors === true) {
-            return data.filter(hasValueAtTimepoint(this.priorTimepointId))
-        }
-
-        return data;
-    },
-
-    unmarked() {
-        const withPriors = true;
-        return this.all(withPriors).filter(hasNoValueAtTimepoint(this.currentTimepointId));;
-    },
-
-    unmarkedTargets() {
-        const withPriors = true;
-        return this.targets(withPriors).filter(hasNoValueAtTimepoint(this.currentTimepointId));;
-    },
-
-    unmarkedNonTargets() {
-        const withPriors = true;
-        return this.nonTargets(withPriors).filter(hasNoValueAtTimepoint(this.currentTimepointId));;
-    },
-
-    // Return only Target Measurements
-    targets(withPriors=false) {
-        let data = Measurements.find({
-            isTarget: true
-        }, this.sortOptions).fetch();
-
-        // If we don't have a prior for this Timepoint,
-        // this filter, we should just return all of the
-        // available Non-Targets measurements
-        if (this.priorTimepointId && withPriors === true) {
-            return data.filter(hasValueAtTimepoint(this.priorTimepointId))
-        }
-
-        return data;
-    },
-
-    // Return only Non-Target Measurements
-    nonTargets(withPriors=false) {
-        let data = Measurements.find({
-            isTarget: false
-        }, this.sortOptions).fetch();
-
-        // If we don't have a prior for this Timepoint,
-        // this filter, we should just return all of the
-        // available Non-Targets measurements
-        if (this.priorTimepointId && withPriors === true) {
-            return data.filter(hasValueAtTimepoint(this.priorTimepointId))
-        }
-
-        return data;
-    },
-
-    // Return only New Lesions
-    newLesions() {
-        // If we are current editing a Baseline we won't have any priors, so newLesions
-        // should return an empty array.
-        if (!this.priorTimepointId) {
-            return [];
-        }
-
-        // Find only lesions that have no value at the previous timepoint
-        return this.all().filter(hasNoValueAtTimepoint(this.priorTimepointId));
-    },
-
-    firstLesion() {
-        return Measurements.findOne({
-            target: true
-        }, this.sortOptions);
-    }
-};

Packages/lesiontracker/client/api/timepoint.js

@@ -1,130 +0,0 @@
-class TimepointApi {
-
-    constructor() {
-        // Run this computation every time the timepoints are changed
-        Tracker.autorun(() => {
-            // Get all the timepoints and store it
-            this.timepoints = new Mongo.Collection(null);
-            const timepoints = Timepoints.find({}, {
-                sort: {
-                    latestDate: -1
-                }
-            }).fetch();
-            _.each(timepoints, timepoint => this.timepoints.insert(timepoint));
-        });
-    }
-
-    // Return all timepoints
-    all() {
-        return this.timepoints.find().fetch();
-    }
-
-    // Return only the current timepoint
-    current() {
-        return this.timepoints.findOne({
-            timepointId: this.currentTimepointId
-        });
-    }
-
-    // Return the prior timepoint
-    prior() {
-        const current = this.current();
-        if (!current) {
-            return;
-        }
-
-        const latestDate = current.latestDate;
-        return this.timepoints.findOne({
-            latestDate: {
-                $lt: latestDate
-            }
-        }, {
-            sort: {
-                latestDate: -1
-            },
-        });
-    }
-
-    // Return only the current and prior Timepoints
-    currentAndPrior() {
-        const timepoints = [];
-
-        const current = this.current();
-        if (current) {
-            timepoints.push(current);
-        }
-
-        const prior = this.prior();
-        if (current && prior && prior._id !== current._id) {
-            timepoints.push(prior);
-        }
-
-        return timepoints;
-    }
-
-    // Return only the baseline timepoint
-    baseline() {
-        return this.timepoints.findOne({
-            timepointType: 'baseline'
-        });
-    }
-
-    // Return only the key timepoints (current, prior, nadir and baseline)
-    key() {
-        // Create a new Mini Mongo Collection to store the result
-        const result = new Mongo.Collection(null);
-
-        // Get all the timepoints
-        const all = this.all();
-
-        // Iterate over each timepoint and insert the key ones in the result
-        _.each(all, (timepoint, index) => {
-            if (index < 2 || index === (all.length - 1)) {
-                result.insert(timepoint);
-            }
-        });
-
-        // Return the resulting timepoints
-        return result.find().fetch();
-    }
-
-    // Return only the timepoints for the given study
-    study(studyInstanceUid) {
-        // Create a new Mini Mongo Collection to store the result
-        const result = new Mongo.Collection(null);
-
-        // Iterate over each timepoint and insert the key ones in the result
-        _.each(this.all(), (timepoint, index) => {
-            if (_.contains(timepoint.studyInstanceUids, studyInstanceUid)) {
-                result.insert(timepoint);
-            }
-        });
-
-        // Return the resulting timepoints
-        return result.find().fetch();
-    }
-
-    // Build the timepoint title based on its date
-    title(timepoint) {
-        const timepointName = getTimepointName(timepoint);
-
-        const all = this.all();
-        let index = -1;
-        _.each(all, (currentTimepoint, currentIndex) => {
-            if (currentTimepoint.timepointId === timepoint.timepointId) {
-                index = currentIndex;
-            }
-        });
-
-        const states = {
-            0: '(Current)',
-            1: '(Prior)'
-        };
-        // TODO: [design] find out how to define the nadir timepoint
-        const parenthesis = states[index] || '';
-        return `${timepointName} ${parenthesis}`;
-    }
-
-}
-
-export { TimepointApi };

Packages/lesiontracker/client/compatibility/crTool.js

@@ -1,10 +0,0 @@
-(function($, cornerstone, cornerstoneMath, cornerstoneTools) {
-
-    'use strict';
-
-    var crToolInterface = cornerstoneTools.crunexTool('crTool');
-    cornerstoneTools.crTool = crToolInterface.crunex;
-    cornerstoneTools.crTool.setConfiguration(crToolInterface.defaultConfiguration);
-    cornerstoneTools.crToolTouch = crToolInterface.crunexTouch;
-
-})($, cornerstone, cornerstoneMath, cornerstoneTools);

Packages/lesiontracker/client/compatibility/exTool.js

@@ -1,9 +0,0 @@
-(function($, cornerstone, cornerstoneMath, cornerstoneTools) {
-
-    'use strict';
-    var exToolInterface = cornerstoneTools.crunexTool('exTool');
-    cornerstoneTools.exTool = exToolInterface.crunex;
-    cornerstoneTools.exTool.setConfiguration(exToolInterface.defaultConfiguration);
-    cornerstoneTools.exToolTouch = exToolInterface.crunexTouch;
-
-})($, cornerstone, cornerstoneMath, cornerstoneTools);

Packages/lesiontracker/client/compatibility/unTool.js

@@ -1,9 +0,0 @@
-(function($, cornerstone, cornerstoneMath, cornerstoneTools) {
-
-    'use strict';
-    var unToolInterface = cornerstoneTools.crunexTool('unTool');
-    cornerstoneTools.unTool = unToolInterface.crunex;
-    cornerstoneTools.unTool.setConfiguration(unToolInterface.defaultConfiguration);
-    cornerstoneTools.unToolTouch = unToolInterface.crunexTouch;
-
-})($, cornerstone, cornerstoneMath, cornerstoneTools);

Packages/lesiontracker/client/components/additionalFindings/additionalFindings.html

@@ -1,55 +0,0 @@
-<template name="additionalFindings">
-    <div class="additionalFindings">
-        <div class="scrollArea">
-            {{#form schema=instance.currentSchema}}
-                <div class="row">
-                    <div class="header">Additional Findings: Baseline</div>
-                    {{>groupRadio labelClass='form-group' key='measurableDisease'}}
-                </div>
-                <div class="row">
-                    <div class="header">Supplementary Measurements</div>
-                    {{>inputSelect class="bone-lesions" labelClass='form-group' key='numberOfBoneLesions' hideSearch=true}}
-                    {{>inputSelect
-                        class="disease-regions"
-                        labelClass='form-group'
-                        key='regionsOfMetastaticDisease'
-                        multiple=true
-                        options=(clone
-                            placeholder='Choose a region'
-                            allowClear=true
-                        )
-                    }}
-                    {{>groupRadio labelClass='form-group' key='tracerRelatedToMetastaticDisease'}}
-                </div>
-                <div class="row">
-                    <div class="header">Image Quality</div>
-                    {{>groupRadio labelClass='form-group' key='acceptableImageQuality'}}
-                    {{>groupRadio labelClass='form-group' key='adequateAnatomicalCoverage'}}
-                    {{>groupRadio labelClass='form-group' key='presenceOfContrast'}}
-                </div>
-                <div class="row">
-                    <div class="header">Additional Screen Captures</div>
-                    <div class="entrySection buttonSection">
-                        <div class="svgContainer">
-                            <svg>
-                                <use xlink:href="/packages/viewerbase/assets/icons.svg#icon-create-screen-capture"></use>
-                            </svg>
-                        </div>
-                        <div class="buttonLabel noselect">Add new screen capture</div>
-                    </div>
-                </div>
-                <div class="row">
-                    <div class="header">Comments</div>
-                    <div class="entrySection buttonSection">
-                        <div class="svgContainer">
-                            <svg>
-                                <use xlink:href="/packages/viewerbase/assets/icons.svg#icon-create-comment"></use>
-                            </svg>
-                        </div>
-                        <div class="buttonLabel noselect">Add a comment</div>
-                    </div>
-                </div>
-            {{/form}}
-        </div>
-    </div>
-</template>

Packages/lesiontracker/client/components/additionalFindings/additionalFindings.js

@@ -1,59 +0,0 @@
-import { Template } from 'meteor/templating';
-import { ReactiveDict } from 'meteor/reactive-dict';
-import { schema as AdditionalFindingsSchema } from 'meteor/lesiontracker/both/schema/additionalFindings';
-
-Template.additionalFindings.onCreated(() => {
-    const instance = Template.instance();
-
-    instance.currentSchema = AdditionalFindingsSchema;
-});
-
-Template.additionalFindings.onRendered(() => {
-    const instance = Template.instance();
-
-    // Get the form component
-    const form = instance.$('form:first').data('component');
-
-    const currentTimepointId = instance.data.currentTimepointId;
-    if (!currentTimepointId) {
-        console.warn('Case has no timepointId');
-        return;
-    }
-
-    const additionalFindings = AdditionalFindings.findOne({
-        timepointId: currentTimepointId
-    });
-
-    if (additionalFindings) {
-        instance.id = additionalFindings._id;
-        form.value(additionalFindings);
-    } else {
-        const defaultData = instance.currentSchema.clean({});
-        form.value(defaultData);
-
-        // Include patientId and timepointId
-        defaultData.patientId = Session.get('patientId');
-        defaultData.timepointId = currentTimepointId;
-
-        // TODO: [design] Turn this into a Meteor Call to insert it on the server
-        instance.id = AdditionalFindings.insert(defaultData);
-    }
-
-    instance.autorun(computation => {
-        // Run this computation everytime the form data is changed
-        form.depend();
-
-        // Stop here if it's the computation's first run
-        if (computation.firstRun) {
-            return;
-        }
-
-        // Get the form data for AdditionalFindings
-        let formData = form.value();
-
-        // TODO: [design] Turn this into a Meteor Call to update it on the server
-        AdditionalFindings.update(instance.id, {
-            $set: formData
-        });
-    });
-});

Packages/lesiontracker/client/components/additionalFindings/additionalFindings.styl

@@ -1,112 +0,0 @@
-@import "{design}/app"
-
-.additionalFindings
-  width: 100%
-  height: 100%
-  background-color: #000000
-
-  .scrollArea
-    height: 100%
-    overflow-x: hidden
-    overflow-y: auto
-    margin-right: -16px
-    padding-right: 16px
-
-    -webkit-overflow-scrolling: touch
-
-    .row
-      margin-right: 0
-      margin-left: 0
-
-    &::-webkit-scrollbar
-      display: none
-
-    .header
-      theme('background-color', '$uiGray')
-      theme('color', '$textPrimaryColor')
-      height: 33px
-      line-height: 33px
-      font-weight: bold
-      font-size: 14px
-      padding: 1px 13px 0
-
-    .form-group
-      theme('color', '$textPrimaryColor')
-      margin-bottom: 0
-      padding: 7px 27px 7px 11px
-      width: 100%
-
-      &:not(:last-child)
-        theme('border-bottom', '%s solid $uiBorderColorDark' % $uiBorderThickness)
-
-      & > .wrapperText
-        display: block
-        font-weight: bold
-        line-height: 15px
-        margin: 10px 2px 8px
-
-      .control-label
-        font-size: 14px
-        font-weight: 100
-        display: inline-block
-        padding: 5px
-
-      .select2
-        margin-bottom: 8px
-        margin-left: 3px
-        margin-top: 5px
-
-      .group-radio
-        height: 30px
-        margin-bottom: 15px
-
-        label
-          display: inline-block
-          float: left
-          font-size: 14px
-          font-weight: 100
-          height: 30px
-          line-height: 30px
-          width: 109px
-
-      .disease-regions + .select2
-        width: 100% !important
-
-      .bone-lesions + .select2
-        width: auto !important
-
-    .buttonSection
-      cursor: pointer
-      height: 90px
-      theme('color', '$defaultColor')
-
-      &:hover
-        theme('color', '$hoverColor')
-
-        .svgContainer
-          svg
-            theme('fill', '$hoverColor')
-
-      &:active
-        theme('color', '$activeColor')
-
-        .svgContainer
-          svg
-            theme('fill', '$activeColor')
-
-      div
-        float: left
-        display: inline-block
-        height: 92px
-
-      .buttonLabel
-        line-height: 92px
-        padding: 0 12px
-
-      .svgContainer
-        padding: 25px 14px
-
-        svg
-          width: 36px
-          height: 36px
-          theme('fill', '$textPrimaryColor')

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

@@ -1,7 +0,0 @@
-<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

@@ -1,32 +0,0 @@
-Template.conformanceCheckFeedback.helpers({
-    validationErrors: function() {
-        // Return validation errors sorted by last added Target
-        var errors = ValidationErrors.find({}, {
-            sort: {
-                prefix: -1,
-                type: 1
-            }
-        });
-
-        Template.instance().validationErrors.set(errors.fetch());
-        return errors;
-    }
-});
-
-Template.conformanceCheckFeedback.events({
-    'mouseenter #conformanceCheckFeedback': function(e, template) {
-        if (template.validationErrors.get().length > 0) {
-            $(e.currentTarget).addClass("conformanceHover");
-        }
-    },
-    'mouseleave #conformanceCheckFeedback': function(e, template) {
-        var conformanceDiv = e.currentTarget;
-        if ($(conformanceDiv).hasClass("conformanceHover")) {
-            $(conformanceDiv).removeClass("conformanceHover");
-        }
-    }
-});
-
-Template.conformanceCheckFeedback.onCreated(function() {
-    this.validationErrors = new ReactiveVar([]);
-});

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

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

Packages/lesiontracker/client/components/flexboxLayout/flexboxLayout.html

@@ -1,18 +0,0 @@
-<template name="flexboxLayout">
-    <div class="viewerSection">
-        <div class="sidebarMenu sidebar-left {{#if leftSidebarOpen}}sidebar-open{{/if}}">
-            {{>studyTimepointBrowser (clone this)}}
-        </div>
-        <div class="mainContent {{#if leftSidebarOpen}}sidebar-left-open{{/if}} {{#if rightSidebarOpen}}sidebar-right-open{{/if}}">
-            {{>viewerMain (clone this)}}
-        </div>
-        <div class="sidebarMenu sidebar-right {{#if or lesionSidebarOpen additionalFindingsSidebarOpen}}sidebar-open{{/if}}">
-            <div class="sidebar-option {{#if lesionSidebarOpen}}active{{/if}}">
-                {{>lesionTable (clone this)}}
-            </div>
-            <div class="sidebar-option {{#if additionalFindingsSidebarOpen}}active{{/if}}">
-                {{>additionalFindings (clone this)}}
-            </div>
-        </div>
-    </div>
-</template>

Packages/lesiontracker/client/components/lesionTable/lesionTable.html

@@ -1,17 +0,0 @@
-<template name="lesionTable">
-    <div id="lesionTableContainer">
-        {{#if this.timepoints.get.length}}
-            <div class="lesionTableLayoutChanger viewerRoundedButtonGroup">
-                {{>roundedButtonGroup buttonGroupData}}
-            </div>
-            <div class="lesionTableTimepointHeaderRow">
-                {{#each this.timepoints.get}}
-                    {{>lesionTableTimepointHeader}}
-                {{/each}}
-            </div>
-            {{>lesionTableView (clone this)}}
-        {{else}}
-            <h3 class="p-x-1 text-center">No associated timepoint</h3>
-        {{/if}}
-    </div>
-</template>

Packages/lesiontracker/client/components/lesionTableHUD/lesionTableHUD.js

@@ -1,48 +0,0 @@
-Template.lesionTableHUD.onCreated(() => {
-    const instance = Template.instance();
-
-    instance.data.timepoints = new ReactiveVar(instance.data.timepointApi.currentAndPrior());
-});
-
-Template.lesionTableHUD.onRendered(() => {
-    const instance = Template.instance();
-    instance.$('#lesionTableHUD').resizable().draggable();
-});
-
-Template.lesionTableHUD.events({
-    'click .buttonClose'(event, instance) {
-        Session.set('lesionTableHudOpen', false);
-    }
-});
-
-Template.lesionTableHUD.helpers({
-    hudHidden() {
-        return Session.get('lesionTableHudOpen') ? 'dialog-open' : 'dialog-closed';
-    },
-    toolbarButtons() {
-        var buttonData = [];
-
-        buttonData.push({
-            id: 'bidirectional',
-            title: 'Target',
-            classes: 'imageViewerTool',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-measure-target'
-        });
-
-        buttonData.push({
-            id: 'nonTarget',
-            title: 'Non-Target',
-            classes: 'imageViewerTool toolbarSectionButton',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-measure-non-target'
-        });
-
-        buttonData.push({
-            id: 'length',
-            title: 'Temp',
-            classes: 'imageViewerTool toolbarSectionButton',
-            svgLink: '/packages/viewerbase/assets/icons.svg#icon-tools-measure-temp'
-        });
-
-        return buttonData;
-    }
-});

Packages/lesiontracker/client/components/lesionTableHeaderRow/lesionTableHeaderRow.html

@@ -1,24 +0,0 @@
-<template name="lesionTableHeaderRow">
-    <div class="lesionTableHeaderRow">
-        {{ #if anyUnmarkedLesionsLeft}}
-        <div class="add js-setTool">
-            <svg>
-                <use xlink:href=/packages/viewerbase/assets/icons.svg#icon-ui-add></use>
-            </svg>
-        </div>
-        {{ /if }}
-        <div class="type">
-            {{type}}
-        </div>
-        <div class="max {{ # if gt numberOfLesions maxNumLesions }}warning{{/if}}">
-        {{ #if maxNumLesions }}
-            <p class="maxNumLesions">
-                Max {{maxNumLesions}}
-            </p>
-        {{/if}}
-        </div>
-        <div class="numberOfLesions">
-            {{numberOfLesions}}
-        </div>
-    </div>
-</template>

Packages/lesiontracker/client/components/lesionTableTimepointCell/lesionTableTimepointCell.html

@@ -1,11 +0,0 @@
-<template name="lesionTableTimepointCell">
-    {{#if hasDataAtThisTimepoint}}
-        <div class="lesionTableTimepointCell" tabindex="1">
-            {{displayData}}
-        </div>
-    {{else}}
-        <div class="lesionTableTimepointCell empty">
-            ...
-        </div>
-    {{/if}}
-</template>

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

@@ -1,39 +0,0 @@
-Template.lesionTableTimepointHeader.helpers({
-    'timepointName': function() {
-        var timepoint = this;
-        return getTimepointName(timepoint);
-    },
-    isLoaded: function() {
-        Session.get('NewSeriesLoaded');
-
-        log.info('ViewerData changed, check for displayed timepoints');
-
-        var timepoint = this;
-
-        var isLoaded = false;
-        var viewports = $('.imageViewerViewport').not('.empty');
-        viewports.each(function(index, element) {
-            var enabledElement = cornerstone.getEnabledElement(element);
-            if (!enabledElement || !enabledElement.image) {
-                return;
-            }
-
-            var study = cornerstoneTools.metaData.get('study', enabledElement.image.imageId);
-
-            var currentTimepoint = Timepoints.findOne({
-                studyInstanceUids: {
-                    $in: [study.studyInstanceUid]
-                }
-            });
-
-            if (currentTimepoint && currentTimepoint._id === timepoint._id) {
-                isLoaded = true;
-
-                // Break the loop
-                return false;
-            }
-        });
-
-        return isLoaded;
-    }
-});

Packages/lesiontracker/client/components/lesionTableView/lesionTableView.html

@@ -1,29 +0,0 @@
-<template name="lesionTableView">
-    <div class="lesionTableView scrollArea">
-        {{>lesionTableHeaderRow id="target"
-                                measurements=targets
-                                currentTimepointId=currentTimepointId
-                                timepointApi=timepointApi}}
-        {{#each target in targets}}
-            {{>lesionTableRow (clone this rowItem=target)}}
-        {{/each}}
-
-        {{>lesionTableHeaderRow id="nonTarget"
-                                measurements=nonTargets
-                                currentTimepointId=currentTimepointId
-                                timepointApi=timepointApi}}
-        {{#each nonTarget in nonTargets}}
-            {{>lesionTableRow (clone this rowItem=nonTarget)}}
-        {{/each}}
-
-        {{#if gt this.timepoints.get.length 1}}
-            {{>lesionTableHeaderRow id="newLesion"
-                                    measurements=newLesions
-                                    currentTimepointId=currentTimepointId
-                                    timepointApi=timepointApi}}
-            {{#each newLesion in newLesions}}
-                {{>lesionTableRow (clone this rowItem=newLesion)}}
-            {{/each}}
-        {{/if}}
-    </div>
-</template>

Packages/lesiontracker/client/components/lesionTableView/lesionTableView.js

@@ -1,23 +0,0 @@
-import { MeasurementApi } from 'meteor/lesiontracker/client/api/measurement';
-
-Template.lesionTableView.helpers({
-    targets() {
-        const withPriors = true;
-        return MeasurementApi.targets(withPriors);
-    },
-
-    nonTargets() {
-        const withPriors = true;
-        return MeasurementApi.nonTargets(withPriors);
-    },
-
-    newLesions() {
-        return MeasurementApi.newLesions();
-    },
-
-    isFollowup() {
-        const instance = Template.instance();
-        const current = instance.data.timepointApi.current();
-        return (current && current.timepointType === 'followup');
-    }
-});

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

@@ -1,42 +0,0 @@
-<template name="lesionTrackerWorklistContextMenu">
-    {{#if uiSettings.studyListFunctionsEnabled}}
-        <div id="studyContextMenu" class="studyContextMenu noselect"
-            oncontextmenu='return false;'
-            unselectable='on'
-            onselectstart='return false;'
-        >
-            <ul>
-                <li>
-                    <a id="viewStudies" type="button"
-                       title="View Studies"
-                    >View</a>
-                    <hr/>
-
-                    <a id="launchStudyAssociation" type="button"
-                       data-toggle="modal"
-                       data-target="#associationModal"
-                       title="Launch Study Association"
-                    >Associate</a>
-                    <a id="launchRemoveAssociation" type="button"
-                       data-toggle="modal"
-                       data-target="#confirmRemoveTimepointAssociation"
-                       title="Remove Timepoint Association"
-                    >Remove Association</a>
-                    <hr/>
-
-                    <a id="viewSeriesDetails" type="button"
-                        title="View Series Details"
-                    >View Series Details</a>
-                    <a class="disabled">Anonymize</a>
-                    <a class="disabled">Send</a>
-                    <hr/>
-
-                    <a id="exportSelectedStudies"
-                        title="Export Selected Studies"
-                    >Export</a>
-                    <a class="disabled">Delete</a>
-                </li>
-            </ul>
-        </div>
-    {{/if}}
-</template>

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

@@ -1,103 +0,0 @@
-// 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);
-    },
-    reviewerTip: function() {
-        var data = this;
-        var study = Studies.findOne({
-            studyInstanceUid: data.studyInstanceUid
-        });
-
-        if (!study) {
-            return;
-        }
-
-        var timepoint = Timepoints.findOne({
-            timepointId: study.timepointId
-        });
-
-        if (!timepoint) {
-            return;
-        }
-
-        var timepointReviewers = Reviewers.findOne({
-            timepointId: timepoint.timepointId
-        });
-        
-        if (!timepointReviewers) {
-            return;
-        }
-
-        return getReviewerTipText(timepointReviewers.reviewers);
-    }
-});
-
-function getReviewerTipText(reviewers) {
-    if (!reviewers || reviewers.length === 0) {
-        return;
-    }
-
-    var newReviewers = reviewers.filter(function(reviewer) {
-        return reviewer.userId !== Meteor.userId();
-    });
-
-    if (newReviewers.length === 0) {
-        return;
-    }
-
-    var tipText = 'The study is being reviewed by ';
-    newReviewers.forEach(function(reviewer, index) {
-        if (reviewer.userId === Meteor.userId()) {
-            return;
-        }
-
-        if (index > 0) {
-            tipText += ',';
-        }
-
-        tipText += reviewer.userName;
-
-    });
-
-    return tipText;
-}
-
-// Observe changes on WorklistTabs
-// remove the current user from Reviewers if tab is removed
-WorklistTabs.find().observe({
-    removed: function(tab) {
-        var contentId = tab.contentid;
-        var timepointIds = ViewerData[contentId].timepointIds;
-        if (timepointIds && timepointIds.length > 0) {
-            timepointIds.forEach(function(timepointId) {
-                // Remove the current user from Reviewers
-                Meteor.call('removeReviewer', timepointId);
-            });
-        }
-    }
-});

Packages/lesiontracker/client/components/viewer/viewer.js

@@ -1,262 +0,0 @@
-import { OHIF } from 'meteor/ohif:core';
-import { TimepointApi } from 'meteor/lesiontracker/client/api/timepoint';
-import { MeasurementApi } from 'meteor/lesiontracker/client/api/measurement';
-
-OHIF.viewer = OHIF.viewer || {};
-OHIF.viewer.loadIndicatorDelay = 3000;
-OHIF.viewer.defaultTool = 'wwwc';
-OHIF.viewer.refLinesEnabled = true;
-OHIF.viewer.cine = {
-    framesPerSecond: 24,
-    loop: true
-};
-
-Session.setDefault('activeViewport', false);
-Session.setDefault('leftSidebar', null);
-Session.setDefault('rightSidebar', null);
-
-Template.viewer.onCreated(() => {
-    const instance = Template.instance();
-
-    ValidationErrors.remove({});
-
-    instance.data.state = new ReactiveDict();
-    instance.data.state.set('leftSidebar', Session.get('leftSidebar'));
-    instance.data.state.set('rightSidebar', Session.get('rightSidebar'));
-
-    instance.subscribe('hangingprotocols');
-
-    Session.set('currentTimepointId', instance.data.currentTimepointId);
-
-    const contentId = instance.data.contentId;
-
-    OHIF.viewer.functionList = $.extend(OHIF.viewer.functionList, {
-        toggleLesionTrackerTools: toggleLesionTrackerTools,
-        clearTools: clearTools,
-        bidirectional: () => {
-            // Used for hotkeys
-            toolManager.setActiveTool('bidirectional');
-        },
-        nonTarget: () => {
-            // 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.bidirectional = 'T'; // Target
-    OHIF.viewer.defaultHotkeys.nonTarget = 'N'; // Non-target
-
-    if (ViewerData[contentId].loadedSeriesData) {
-        log.info('Reloading previous loadedSeriesData');
-        OHIF.viewer.loadedSeriesData = ViewerData[contentId].loadedSeriesData;
-
-    } else {
-        log.info('Setting default ViewerData');
-        OHIF.viewer.loadedSeriesData = {};
-        ViewerData[contentId].loadedSeriesData = {};
-        Session.set('ViewerData', ViewerData);
-    }
-
-    Session.set('activeViewport', ViewerData[contentId].activeViewport || false);
-
-    // Set lesion tool buttons as disabled if pixel spacing is not available for active element
-    instance.autorun(pixelSpacingAutorunCheck);
-
-    // Update the ViewerStudies collection with the loaded studies
-    ViewerStudies.remove({});
-
-    instance.data.studies.forEach(study => {
-        study.selected = true;
-        study.displaySets = createStacks(study);
-        ViewerStudies.insert(study);
-    });
-
-    const patientId = instance.data.studies[0].patientId;
-    Session.set('patientId', patientId);
-
-    instance.autorun(() => {
-        const dataContext = Template.currentData();
-        instance.subscribe('singlePatientAssociatedStudies', dataContext.studies[0].patientId);
-        instance.subscribe('singlePatientTimepoints', dataContext.studies[0].patientId);
-        instance.subscribe('singlePatientMeasurements', dataContext.studies[0].patientId);
-        instance.subscribe('singlePatientImageMeasurements', dataContext.studies[0].patientId);
-        instance.subscribe('singlePatientAdditionalFindings', dataContext.studies[0].patientId);
-
-        if (instance.subscriptionsReady()) {
-            // Set buttons as enabled/disabled when Timepoints collection is ready
-            timepointAutoCheck(dataContext);
-
-            // Wait until the Timepoint subscription is ready to initialize the TimepointApi
-            instance.data.timepointApi = new TimepointApi();
-            instance.data.timepointApi.currentTimepointId = instance.data.currentTimepointId;
-
-            // Provide the necessary data to the Measurement API
-            MeasurementApi.currentTimepointId = instance.data.currentTimepointId;
-            const prior = instance.data.timepointApi.prior();
-            if (prior) {
-                MeasurementApi.priorTimepointId = prior.timepointId;
-            }
-
-            TrialResponseCriteria.validateAllDelayed();
-
-            ViewerStudies.find().observe({
-                added: study => {
-                    // Find the relevant timepoint given the newly added study
-                    const timepoint = Timepoints.findOne({
-                        studyInstanceUids: {
-                            $in: [study.studyInstanceUid]
-                        }
-                    });
-
-                    if (!timepoint) {
-                        log.warn('Study added to Viewer has not been associated!');
-                        return;
-                    }
-
-                    // Update the added document with its related timepointId
-                    ViewerStudies.update(study._id, {
-                        $set: {
-                            timepointId: timepoint.timepointId
-                        }
-                    });
-                }
-            });
-
-            ImageMeasurements.find().observe({
-                added: data => {
-                    if (data.clientId === ClientId) {
-                        return;
-                    }
-
-                    syncImageMeasurementAndToolData(data);
-
-                    // Update each displayed viewport
-                    updateAllViewports();
-                },
-                changed: data => {
-                    if (data.clientId === ClientId) {
-                        return;
-                    }
-
-                    syncImageMeasurementAndToolData(data);
-
-                    // Update each displayed viewport
-                    updateAllViewports();
-                },
-                removed: data => {
-                    if (data.clientId === ClientId) {
-                        return;
-                    }
-
-                    removeToolDataWithMeasurementId(data.imageId, data.toolType, data.id);
-
-                    // Update each displayed viewport
-                    updateAllViewports();
-                }
-            });
-
-            Measurements.find().observe({
-                added: data => {
-                    if (data.clientId === ClientId) {
-                        TrialResponseCriteria.validateAllDelayed();
-                        return;
-                    }
-
-                    log.info('Measurement added');
-
-                    // This is used to re-add tools from the database into the
-                    // Cornerstone ToolData structure
-                    syncMeasurementAndToolData(data);
-
-                    // Update each displayed viewport
-                    updateAllViewports();
-                },
-                changed: data => {
-                    if (data.clientId === ClientId) {
-                        TrialResponseCriteria.validateAllDelayed();
-                        return;
-                    }
-
-                    log.info('Measurement changed');
-
-                    // This is used to update changed tools from the database
-                    // in the Cornerstone ToolData structure
-                    syncMeasurementAndToolData(data);
-
-                    // Update each displayed viewport
-                    updateAllViewports();
-
-                    TrialResponseCriteria.validateAllDelayed();
-                },
-                removed: data => {
-                    log.info('Measurement removed');
-
-                    // Check that this Measurement actually contains timepoint data
-                    if (!data || !data.timepoints) {
-                        return;
-                    }
-
-                    // Get the Measurement ID and relevant tool so we can remove
-                    // tool data for this Measurement
-                    const measurementId = data._id;
-                    const toolType = data.toolType;
-
-                    // Remove the measurement from all the imageIds on which it exists
-                    // as toolData
-                    Object.keys(data.timepoints).forEach(timepointId => {
-                        // Clear the toolData for this timepoint
-                        const imageId = data.timepoints[timepointId].imageId;
-                        removeToolDataWithMeasurementId(imageId, toolType, measurementId);
-
-                        // Set reviewer for this timepoint
-                        if (data.timepoints[timepointId].studyInstanceUid) {
-                            Meteor.call('setReviewer', data.timepoints[timepointId].studyInstanceUid);
-                        }
-                    });
-
-                    // Sync database data with toolData for all the measurements
-                    // that have just been updated
-
-                    // Note that here we need to use greater than and equals to
-                    // find the Measurements, whereas on the server it's
-                    // only "greater than", since inside this callback the
-                    // Measurements have already been decremented.
-                    const measurements = Measurements.find({
-                        patientId: data.patientId,
-                        lesionNumberAbsolute: {
-                            $gte: data.lesionNumberAbsolute
-                        }
-                    });
-
-                    measurements.forEach(measurement => {
-                        syncMeasurementAndToolData(measurement);
-                    });
-
-                    // Update each displayed viewport
-                    updateAllViewports();
-
-                    ValidationErrors.remove({
-                        measurementId: data._id
-                    });
-
-                    TrialResponseCriteria.validateAll();
-                }
-            });
-        }
-    });
-});
-
-Template.viewer.events({
-    'CornerstoneToolsMeasurementAdded .imageViewerViewport'(event, instance, eventData) {
-        handleMeasurementAdded(event, eventData);
-    },
-    'CornerstoneToolsMeasurementModified .imageViewerViewport'(event, instance, eventData) {
-        handleMeasurementModified(event, eventData);
-    },
-    'CornerstoneToolsMeasurementRemoved .imageViewerViewport'(event, instance, eventData) {
-        handleMeasurementRemoved(event, eventData);
-    }
-});

Packages/lesiontracker/lib/LesionManager.js

@@ -1,210 +0,0 @@
-measurementValuesByType = {
-    bidirectional: [
-        'shortestDiameter',
-        'longestDiameter'
-    ],
-    nonTarget: ['response'],
-    crTool: ['response'],
-    exTool: ['response'],
-    unTool: ['response'],
-    length: ['length'],
-    ellipticalRoi: [
-        'area',
-        'mean',
-        'stdev'
-    ]
-
-};
-
-/**
- * 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.toolType) {
-        // For debugging, might want to switch to measurement types later
-        lesionData.toolType = lesionData.isTarget ? 'bidirectional' : 'nonTarget';
-    }
-
-    // Populate this timepoint's data with whichever values
-    // are stored for this Measurement type
-    var values = measurementValuesByType[lesionData.toolType];
-    values.forEach(function(valueName) {
-        timepointData[valueName] = lesionData[valueName];
-    });
-
-    // 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,
-            toolType: lesionData.toolType
-        };
-        if (lesionData.toolType) {
-            measurement.toolType = lesionData.toolType;
-        }
-
-        // Retrieve the location name given the locationUID
-        if (lesionData.locationUID !== undefined) {
-            var locationObj = LesionLocations.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.clientId = ClientId;
-
-        // 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?)
-        log.info('LesionManager inserting Measurement');
-        measurement.id = Measurements.insert(measurement);
-    } else {
-        lesionData.id = existingMeasurement._id;
-        lesionData.isNodal = existingMeasurement.isNodal;
-
-        if (_.isEqual(existingMeasurement.timepoints[timepoint.timepointId], timepointData)) {
-            return;
-        }
-
-        // Update timepoints from lesion data
-        existingMeasurement.timepoints[timepoint.timepointId] = timepointData;
-
-        log.info('LesionManager updating Measurement');
-        Measurements.update(existingMeasurement._id, {
-            $set: {
-                timepoints: existingMeasurement.timepoints,
-                clientId: ClientId
-            }
-        });
-    }
-}
-
-/**
- * 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.locationId;
-}
-
-LesionManager = {
-    updateLesionData: updateLesionData,
-    getNewLesionNumber: getNewLesionNumber,
-    lesionNumberExists: lesionNumberExists
-};

Packages/lesiontracker/lib/calculateTotalLesionBurden.js

@@ -1,59 +0,0 @@
-/**
- * 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.shortestDiameter);
-
-                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

@@ -1,36 +0,0 @@
-clearMeasurementTimepointData = function(measurementId, timepointId) {
-    var data = Measurements.findOne(measurementId);
-
-    // Check that this Measurement actually contains data for this timepoint
-    if (!data || !data.timepoints[timepointId]) {
-        return;
-    }
-
-    // Clear the Measurement data for this timepoint
-    var imageId = data.timepoints[timepointId].imageId;
-    var toolType = data.toolType;
-    removeToolDataWithMeasurementId(imageId, toolType, measurementId);
-
-    // Update any viewports that are currently displaying this imageId
-    var enabledElements = cornerstone.getEnabledElementsByImageId(imageId);
-    enabledElements.forEach(function(enabledElement) {
-        cornerstone.updateImage(enabledElement.element);
-    });
-
-    delete data.timepoints[timepointId];
-
-    if (!Object.keys(data.timepoints).length) {
-        Meteor.call('removeMeasurement', measurementId, function(error, response) {
-            if (error) {
-                log.warn(error);
-            }
-        });
-    } else {
-        // Update the Timepoint object of the Measurement document
-        Measurements.update(measurementId, {
-            $set: {
-                timepoints: data.timepoints
-            }
-        });
-    }
-};

Packages/lesiontracker/lib/clearTools.js

@@ -1,58 +0,0 @@
-clearTools = function() {
-    var patientId = Session.get('patientId');
-    var toolTypes = [ 'bidirectional', 'nonTarget', 'length', 'ellipticalRoi', 'crTool', 'unTool', 'exTool' ];
-    var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
-    var toolStateKeys = Object.keys(toolState).slice(0);
-
-    var viewportElements = $('.imageViewerViewport').not('.empty');
-    var seriesInstanceUids = []; // Holds seriesInstanceUid of imageViewerViewport elements
-    viewportElements.each(function(index, element) {
-        var enabledElement = cornerstone.getEnabledElement(element);
-        var study = cornerstoneTools.metaData.get('study', enabledElement.image.imageId);
-        if (!study) {
-            return;
-        }
-        // Set reviewer for this timepoint
-        if (study.studyInstanceUid) {
-            Meteor.call('setReviewer',study.studyInstanceUid);
-        }
-        var series = cornerstoneTools.metaData.get('series', enabledElement.image.imageId);
-        if (!series) {
-            return;
-        }
-        
-        seriesInstanceUids.push(series.seriesInstanceUid);
-    });
-
-    // Set null array for toolState data found by imageId and toolType
-    toolStateKeys.forEach(function(imageId) {
-        toolTypes.forEach(function(toolType) {
-            var toolTypeData = toolState[imageId][toolType];
-            if (toolTypeData && toolTypeData.data.length > 0) {
-                var series = cornerstoneTools.metaData.get('series', imageId);
-                if (!series) {
-                    return;
-                }
-
-                // If seriesInstanceUid is found in seriesInstanceUids, set toolState data as null
-                if (seriesInstanceUids.indexOf(series.seriesInstanceUid) > -1) {
-                    toolState[imageId][toolType] = {
-                        data: []
-                    };
-                }
-            }
-        });
-    });
-
-    // Update imageViewerViewport elements to remove lesions on current image
-    viewportElements.each(function(index, element) {
-        cornerstone.updateImage(element);
-    });
-
-    // Remove patient's measurements
-    Meteor.call('removeMeasurementsByPatientId', patientId);
-    Meteor.call('removeImageMeasurementsByPatientId', patientId);
-
-    // Clear all validation errors
-    ValidationErrors.remove({});
-};

Packages/lesiontracker/lib/handleMeasurementAdded.js

@@ -1,41 +0,0 @@
-handleMeasurementAdded = function(e, eventData) {
-    var measurementData = eventData.measurementData;
-    switch (measurementData.toolType) {
-        case 'nonTarget':
-        case 'bidirectional':
-        case 'crTool':
-        case 'unTool':
-        case 'exTool':
-            log.info('CornerstoneToolsMeasurementAdded');
-            LesionManager.updateLesionData(measurementData);
-            TrialResponseCriteria.validateDelayed(measurementData);
-            // Set reviewer for this timepoint
-            if (measurementData.studyInstanceUid) {
-                Meteor.call('setReviewer', measurementData.studyInstanceUid);
-            }
-
-            break;
-        case 'ellipticalRoi':
-        case 'length':
-            var enabledElement = cornerstone.getEnabledElement(eventData.element);
-            var imageId = enabledElement.image.imageId;
-
-            // Get the studyInstanceUid and series metaData
-            var study = cornerstoneTools.metaData.get('study', imageId);
-            var series = cornerstoneTools.metaData.get('series', imageId);
-
-            // Add the relevant metaData to this ImageMeasurement's toolData
-            measurementData.clientId = ClientId;
-            measurementData.imageId = imageId;
-            measurementData.toolType = eventData.toolType;
-            measurementData.patientId = study.patientId;
-            measurementData.studyInstanceUid = study.studyInstanceUid;
-            measurementData.seriesInstanceUid = series.seriesInstanceUid;
-
-            // Create the ImageMeasurement in the database
-            measurementData._id = ImageMeasurements.insert(measurementData);
-
-            break;
-    }
-
-};

Packages/lesiontracker/lib/handleMeasurementModified.js

@@ -1,44 +0,0 @@
-handleMeasurementModified = function(e, eventData) {
-    var measurementData = eventData.measurementData;
-    switch (measurementData.toolType) {
-        case 'nonTarget':
-        case 'bidirectional':
-        case 'crTool':
-        case 'unTool':
-        case 'exTool':
-            log.info('CornerstoneToolsMeasurementModified');
-            LesionManager.updateLesionData(measurementData);
-            TrialResponseCriteria.validateDelayed(measurementData);
-            // Set reviewer for this timepoint
-            if (measurementData.studyInstanceUid) {
-                Meteor.call('setReviewer',measurementData.studyInstanceUid);
-            }
-            break;
-        case 'ellipticalRoi':
-        case 'length':
-            var enabledElement = cornerstone.getEnabledElement(eventData.element);
-            var imageId = enabledElement.image.imageId;
-
-            // Get the studyInstanceUid and series metaData
-            var study = cornerstoneTools.metaData.get('study', imageId);
-            var series = cornerstoneTools.metaData.get('series', imageId);
-
-            // Add the relevant metaData to this ImageMeasurement's toolData
-            measurementData.clientId = ClientId;
-            measurementData.imageId = imageId;
-            measurementData.toolType = eventData.toolType;
-            measurementData.patientId = study.patientId;
-            measurementData.studyInstanceUid = study.studyInstanceUid;
-            measurementData.seriesInstanceUid = series.seriesInstanceUid;
-            var toUpdate = $.extend({}, measurementData);
-
-            // Remove the Mongo _id otherwise it will complain when we try to 'mod' it.
-            delete toUpdate._id;
-
-            // Update the ImageMeasurement in the database
-            ImageMeasurements.update(measurementData._id, {
-                $set: toUpdate
-            });
-            break;
-    }
-};

Packages/lesiontracker/lib/handleMeasurementRemoved.js

@@ -1,27 +0,0 @@
-handleMeasurementRemoved = function(e, eventData) {
-    var measurementData = eventData.measurementData;
-
-    switch (eventData.toolType) {
-        case 'nonTarget':
-        case 'bidirectional':
-        case 'crTool':
-        case 'unTool':
-        case 'exTool':
-            log.info('CornerstoneToolsMeasurementRemoved');
-
-            var measurement = Measurements.findOne(measurementData.id, {
-                reactive: false
-            });
-
-            if (!measurement) {
-                return;
-            }
-            // Set reviewer for this timepoint
-            if (measurementData.studyInstanceUid) {
-                Meteor.call('setReviewer', measurementData.studyInstanceUid);
-            }
-
-            clearMeasurementTimepointData(measurement._id, measurementData.timepointId);
-            break;
-    }
-};

Packages/lesiontracker/lib/syncImageMeasurementAndToolData.js

@@ -1,59 +0,0 @@
-syncImageMeasurementAndToolData = function(measurement) {
-    // TODO: Refactor this to merge it with syncMeasurementAndToolData somehow
-    log.info('syncImageMeasurementAndToolData');
-
-    var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
-
-    var imageId = measurement.imageId;
-    var toolType = measurement.toolType;
-
-    // If no tool state exists for this imageId, create an empty object to store it
-    if (!toolState[imageId]) {
-        toolState[imageId] = {};
-    }
-
-    // Check if we already have toolData for this imageId and toolType
-    if (toolState[imageId][toolType] &&
-        toolState[imageId][toolType].data &&
-        toolState[imageId][toolType].data.length) {
-        // If we have toolData, we should search it for any toolData
-        // related to the current ImageMeasurement
-        var toolData = toolState[imageId][toolType].data;
-
-        // Create a flag so we know if we have successfully updated
-        // this ImageMeasurement's timepoint data in the toolData
-        var alreadyExists = false;
-
-        // Loop through the toolData to search for this ImageMeasurement
-        toolData.forEach(function(tool) {
-            // Break the loop if this isn't the ImageMeasurement we are looking for
-            if (tool._id !== measurement._id) {
-                return;
-            }
-
-            // If we find the ImageMeasurement, set the flag to True
-            alreadyExists = true;
-
-            // Update the toolData from the ImageMeasurement data
-            $.extend(tool, measurement);
-            return false;
-        });
-
-        // If we found the ImageMeasurement we intended to update, we can stop
-        // this function here
-        if (alreadyExists === true) {
-            return;
-        }
-    } else {
-        // If no toolData exists for this toolType, create an empty array to hold some
-        toolState[imageId][toolType] = {
-            data: []
-        };
-    }
-
-    // If we have reached this point, it means we haven't found the ImageMeasurement we are
-    // looking for in the current toolData. This means we need to add it.
-
-    // Add the ImageMeasurementData into the toolData for this imageId
-    toolState[imageId][toolType].data.push(measurement);
-};

Packages/lesiontracker/lib/syncMeasurementAndToolData.js

@@ -1,90 +0,0 @@
-syncMeasurementAndToolData = function(measurement) {
-    log.info('syncMeasurementAndToolData');
-
-    // Check what toolType we should be adding this to, based on the isTarget value
-    // of the stored Measurement
-    var toolType = measurement.toolType;
-
-    // Loop through the timepoint data for this measurement
-    Object.keys(measurement.timepoints).forEach(function(key) {
-        var timepointData = measurement.timepoints[key];
-        var imageId = timepointData.imageId;
-
-        // Sync the Cornerstone ToolData with this Measurement's timepoint-specific data
-        syncTimepointDataWithToolData(measurement, timepointData, imageId, toolType);
-    });
-};
-
-function syncTimepointDataWithToolData(measurement, timepointData, imageId, toolType) {
-    // Get the global imageId-specific toolState from Cornerstone Tools
-    var toolState = cornerstoneTools.globalImageIdSpecificToolStateManager.toolState;
-
-    // If no tool state exists for this imageId, create an empty object to store it
-    if (!toolState[imageId]) {
-        toolState[imageId] = {};
-    }
-
-    // Check if we already have toolData for this imageId and toolType
-    if (toolState[imageId][toolType] &&
-        toolState[imageId][toolType].data &&
-        toolState[imageId][toolType].data.length) {
-
-        // If we have toolData, we should search it for any toolData
-        // related to the current Measurement
-        var toolData = toolState[imageId][toolType].data;
-
-        // Create a flag so we know if we have successfully updated
-        // this Measurement's timepoint data in the toolData
-        var alreadyExists = false;
-
-        // Loop through the toolData to search for this Measurement's
-        // timepoint data
-        toolData.forEach(function(tool) {
-            // Break the loop if this isn't the Measurement we are looking for
-            if (tool.id !== measurement._id) {
-                return;
-            }
-
-            // If we find the Measurement, set the flag to True
-            alreadyExists = true;
-
-            // Update the toolData from the Measurement data and
-            // timepoint-specific data from this Measurement
-            tool.lesionNumber = measurement.lesionNumber;
-            tool.isTarget = measurement.isTarget;
-            tool.active = timepointData.active;
-            tool.visible = timepointData.visible;
-            tool.isDeleted = timepointData.isDeleted;
-            tool.handles = timepointData.handles;
-            tool.toolType = measurement.toolType;
-            return false;
-        });
-
-        // If we found the Measurement we intended to update, we can stop
-        // this function here
-        if (alreadyExists === true) {
-            return;
-        }
-    } else {
-        // If no toolData exists for this toolType, create an empty array to hold some
-        toolState[imageId][toolType] = {
-            data: []
-        };
-    }
-
-    // If we have reached this point, it means we haven't found the Measurement we are
-    // looking for in the current toolData. This means we need to add it.
-
-    // First, create the measurementData structure based on the lesion data at this timepoint.
-    var tool = timepointData;
-    tool.lesionNumber = measurement.lesionNumber;
-    tool.isTarget = measurement.isTarget;
-    tool.location = measurement.location;
-    tool.locationUID = measurement.locationUID;
-    tool.patientId = measurement.patientId;
-    tool.id = measurement._id;
-    tool.toolType = measurement.toolType;
-
-    // Add the measurementData into the toolData for this imageId
-    toolState[imageId][toolType].data.push(tool);
-}

Packages/lesiontracker/lib/timepointAutoCheck.js

@@ -1,42 +0,0 @@
-// If timepoint is baseline, sets lesion tool as active tool
-setTimepointTools = function(timepoint) {
-    if (!timepoint) {
-        return;
-    }
-
-    var disabledBaselineTools = ["crunexTools"];
-    var states = toolManager.getToolDefaultStates();
-    var disabledToolButtons = states.disabledToolButtons;
-
-    if (timepoint.timepointType === "baseline") {
-        // Set active tool as lesion tool
-        toolManager.setActiveTool('bidirectional');
-        disabledBaselineTools.forEach(function(tool) {
-            var index = disabledToolButtons.indexOf(tool);
-            if (index === -1) {
-                disabledToolButtons.push(tool);
-            }
-        });
-    } else {
-        toolManager.setActiveTool(toolManager.getDefaultTool());
-        // Remove disabled baseline tools
-        disabledBaselineTools.forEach(function(tool) {
-            var index = disabledToolButtons.indexOf(tool);
-            if (index !== -1) {
-                disabledToolButtons.splice(index, 1);
-            }
-        });
-    }
-
-    states.disabledToolButtons = disabledToolButtons;
-    toolManager.setToolDefaultStates(states);
-};
-
-timepointAutoCheck = function(templateData) {
-    if (templateData && templateData.timepointIds) {
-        templateData.timepointIds.forEach(function(timepointId) {
-            var timepoint = Timepoints.findOne({timepointId: timepointId});
-            setTimepointTools(timepoint);
-        });
-    }
-};

Packages/lesiontracker/lib/updateRelatedElements.js

@@ -1,13 +0,0 @@
-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/worklist/worklistModification.js

@@ -1,73 +0,0 @@
-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
-        open(data.studyInstanceUid, title);
-        return;
-    }
-
-    // Find the relevant timepoint given the clicked-on study
-    var timepoint = Timepoints.findOne({
-        studyInstanceUids: {
-            $in: [data.studyInstanceUid]
-        }
-    });
-
-    if (!timepoint) {
-        open(data.studyInstanceUid, title);
-        return;
-    }
-
-    // Add the Timepoint name to the Patient name to create the tab title
-    title += ' ' + getTimepointName(timepoint);
-
-    openNewTabWithTimepoint(timepoint.timepointId, title);
-}
-
-/**
- * Opens a study
- *
- * @param studyInstanceUid The UID of the Study to be opened
- * @param title The title to be used for the tab heading
- */
-function open(studyInstanceUid, title) {
-    var contentid = 'viewerTab';
-
-    WorklistTabs.remove({});
-    
-    // Create a new entry in the WorklistTabs Collection
-    WorklistTabs.insert({
-        title: title,
-        contentid: contentid,
-        studyInstanceUid: studyInstanceUid,
-        active: false
-    });
-
-    ViewerData = window.ViewerData || ViewerData;
-
-    // Update the ViewerData global object
-    ViewerData[contentid] = {
-        title: title,
-        contentid: contentid,
-        studyInstanceUids: [studyInstanceUid]
-    };
-
-    // Switch to the new tab
-    console.log('open');
-    switchToTab(contentid);
-}

Packages/lesiontracker/package.js

@@ -1,293 +0,0 @@
-Package.describe({
-    name: 'lesiontracker',
-    summary: 'OHIF Lesion Tracker Tools',
-    version: '0.0.1'
-});
-
-Package.onUse(function(api) {
-    api.versionsFrom('1.4');
-
-    api.use('ecmascript');
-    api.use('standard-app-packages');
-    api.use('jquery');
-    api.use('stylus');
-    api.use('design');
-
-    api.use('validatejs');
-
-    // Schema for Data Models
-    api.use('aldeed:simple-schema');
-
-    // 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 packages
-    api.use('ohif:core');
-    api.use('worklist');
-    api.use('cornerstone');
-
-    api.addFiles('log.js', [ 'client', 'server' ]);
-
-    // Schema
-    api.addFiles('both/schema/additionalFindings.js', [ 'client', 'server' ]);
-
-    // Client-side collections
-    api.addFiles('client/collections/LesionLocations.js', 'client');
-    api.addFiles('client/collections/LocationResponses.js', 'client');
-    api.addFiles('client/collections/subscriptions.js', 'client');
-
-    // Additional Custom Cornerstone Tools for Lesion Tracker
-    api.addFiles([
-        'client/compatibility/bidirectionalTool.js',
-        'client/compatibility/nonTargetTool.js',
-        'client/compatibility/scaleOverlayTool.js',
-        'client/compatibility/deleteLesionKeyboardTool.js',
-        'client/compatibility/crunexTool.js',
-        'client/compatibility/crTool.js',
-        'client/compatibility/unTool.js',
-        'client/compatibility/exTool.js'
-    ], 'client', {
-        bare: true
-    });
-
-    api.addFiles('client/tools.js', 'client');
-
-    // UI Components
-    api.addFiles('client/components/viewer/viewer.html', 'client');
-    api.addFiles('client/components/viewer/viewer.styl', 'client');
-    api.addFiles('client/components/viewer/viewer.js', 'client');
-
-    api.addFiles('client/components/flexboxLayout/flexboxLayout.html', 'client');
-    api.addFiles('client/components/flexboxLayout/flexboxLayout.styl', 'client');
-    api.addFiles('client/components/flexboxLayout/flexboxLayout.js', 'client');
-
-    api.addFiles('client/components/toolbarSection/toolbarSection.html', 'client');
-    api.addFiles('client/components/toolbarSection/toolbarSection.styl', 'client');
-    api.addFiles('client/components/toolbarSection/toolbarSection.js', 'client');
-
-    api.addFiles('client/components/radialProgressBar/radialProgressBar.html', 'client');
-    api.addFiles('client/components/radialProgressBar/radialProgressBar.styl', 'client');
-    api.addFiles('client/components/radialProgressBar/radialProgressBar.js', 'client');
-
-    api.addFiles('client/components/caseProgress/caseProgress.html', 'client');
-    api.addFiles('client/components/caseProgress/caseProgress.styl', 'client');
-    api.addFiles('client/components/caseProgress/caseProgress.js', 'client');
-
-    api.addFiles('client/components/lesionTracker/lesionTracker.html', 'client');
-    api.addFiles('client/components/lesionTracker/lesionTracker.styl', 'client');
-    api.addFiles('client/components/lesionTracker/lesionTracker.js', 'client');
-
-    api.addFiles('client/components/additionalFindings/additionalFindings.html', 'client');
-    api.addFiles('client/components/additionalFindings/additionalFindings.styl', 'client');
-    api.addFiles('client/components/additionalFindings/additionalFindings.js', 'client');
-
-    api.addFiles('client/components/studySeriesQuickSwitch/studySeriesQuickSwitch.html', 'client');
-    api.addFiles('client/components/studySeriesQuickSwitch/studySeriesQuickSwitch.styl', 'client');
-    api.addFiles('client/components/studySeriesQuickSwitch/studySeriesQuickSwitch.js', '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/activeEntry/activeEntry.styl', 'client');
-    api.addFiles('client/components/activeEntry/activeEntry.js', 'client');
-
-    api.addFiles('client/components/activeEntry/activeEntrySignIn/activeEntrySignIn.js', 'client');
-
-    api.addFiles('client/components/hipaaLogPage/hipaaLogPage.styl', 'client');
-    api.addFiles('client/components/hipaaLogPage/hipaaLogPage.js', '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/recistDescription/recistDescription.html', 'client');
-    api.addFiles('client/components/irRCDescription/irRCDescription.html', 'client');
-
-    api.addFiles('client/components/lesionLocationDialog/lesionLocationDialog.html', 'client');
-    api.addFiles('client/components/lesionLocationDialog/lesionLocationDialog.js', 'client');
-    api.addFiles('client/components/lesionLocationDialog/lesionLocationDialog.styl', 'client');
-
-    api.addFiles('client/components/lesionTableView/lesionTableView.html', 'client');
-    api.addFiles('client/components/lesionTableView/lesionTableView.styl', 'client');
-    api.addFiles('client/components/lesionTableView/lesionTableView.js', 'client');
-
-    api.addFiles('client/components/lesionTable/lesionTable.html', 'client');
-    api.addFiles('client/components/lesionTable/lesionTable.styl', 'client');
-    api.addFiles('client/components/lesionTable/lesionTable.js', 'client');
-
-    api.addFiles('client/components/lesionTableHUD/lesionTableHUD.html', 'client');
-    api.addFiles('client/components/lesionTableHUD/lesionTableHUD.styl', 'client');
-    api.addFiles('client/components/lesionTableHUD/lesionTableHUD.js', 'client');
-
-    api.addFiles('client/components/lesionTableRow/lesionTableRow.html', 'client');
-    api.addFiles('client/components/lesionTableRow/lesionTableRow.styl', 'client');
-    api.addFiles('client/components/lesionTableRow/lesionTableRow.js', 'client');
-
-    api.addFiles('client/components/lesionTableHeaderRow/lesionTableHeaderRow.html', 'client');
-    api.addFiles('client/components/lesionTableHeaderRow/lesionTableHeaderRow.styl', 'client');
-    api.addFiles('client/components/lesionTableHeaderRow/lesionTableHeaderRow.js', 'client');
-
-    api.addFiles('client/components/lesionTableTimepointCell/lesionTableTimepointCell.html', 'client');
-    api.addFiles('client/components/lesionTableTimepointCell/lesionTableTimepointCell.styl', 'client');
-    api.addFiles('client/components/lesionTableTimepointCell/lesionTableTimepointCell.js', 'client');
-
-    api.addFiles('client/components/lesionTableTimepointHeader/lesionTableTimepointHeader.html', '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');
-    api.addFiles('client/components/nonTargetLesionDialog/nonTargetLesionDialog.js', 'client');
-
-    api.addFiles('client/components/studyTimepointBrowser/studyTimepoint.html', 'client');
-    api.addFiles('client/components/studyTimepointBrowser/studyTimepoint.styl', 'client');
-    api.addFiles('client/components/studyTimepointBrowser/studyTimepoint.js', 'client');
-
-    api.addFiles('client/components/studyTimepointBrowser/studyTimepointBrowser.html', 'client');
-    api.addFiles('client/components/studyTimepointBrowser/studyTimepointBrowser.styl', 'client');
-    api.addFiles('client/components/studyTimepointBrowser/studyTimepointBrowser.js', 'client');
-
-    api.addFiles('client/components/studyTimepointBrowser/studyTimepointStudy.html', 'client');
-    api.addFiles('client/components/studyTimepointBrowser/studyTimepointStudy.styl', 'client');
-    api.addFiles('client/components/studyTimepointBrowser/studyTimepointStudy.js', 'client');
-
-    api.addFiles('client/components/studyAssociationTable/studyAssociationTable.html', 'client');
-    api.addFiles('client/components/studyAssociationTable/studyAssociationTable.styl', 'client');
-    api.addFiles('client/components/studyAssociationTable/studyAssociationTable.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');
-
-    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/measureFlow/measureFlow.html', 'client');
-    api.addFiles('client/components/measureFlow/measureFlow.styl', 'client');
-    api.addFiles('client/components/measureFlow/measureFlow.js', 'client');
-
-    api.addFiles('client/components/timeoutCountdownDialog/timeoutCountdownDialog.html', 'client');
-    api.addFiles('client/components/timeoutCountdownDialog/timeoutCountdownDialog.styl', 'client');
-    api.addFiles('client/components/timeoutCountdownDialog/timeoutCountdownDialog.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.js', 'client');
-
-    api.addFiles('client/components/userAccountMenu/userAccountMenu.html', 'client');
-    api.addFiles('client/components/userAccountMenu/userAccountMenu.styl', 'client');
-    api.addFiles('client/components/userAccountMenu/userAccountMenu.js', 'client');
-
-    api.addFiles('client/components/confirmRemoveTimepointAssociation/confirmRemoveTimepointAssociation.html', 'client');
-    api.addFiles('client/components/confirmRemoveTimepointAssociation/confirmRemoveTimepointAssociation.js', 'client');
-
-    api.addFiles('client/components/lastLoginModal/lastLoginModal.html', 'client');
-
-    api.addFiles('client/components/emailVerification/emailVerification.html', 'client');
-    api.addFiles('client/components/emailVerification/emailVerification.styl', 'client');
-    api.addFiles('client/components/emailVerification/emailVerification.js', 'client');
-
-    // Server functions
-    api.addFiles('server/publications.js', 'server');
-    api.addFiles('server/methods.js', [ 'server' ]);
-    api.addFiles('server/reviewers.js', [ 'server' ]);
-    api.addFiles('server/createDemoUser.js', [ 'server' ]);
-
-    // 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/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/convertToNonTarget.js', 'client');
-    api.addFiles('lib/convertNonTarget.js', 'client');
-    api.addFiles('lib/timepointAutoCheck.js', 'client');
-
-    api.addFiles('lib/syncMeasurementAndToolData.js', 'client');
-    api.addFiles('lib/syncImageMeasurementAndToolData.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');
-
-    // API classes
-    api.addFiles('client/api/timepoint.js');
-    api.addFiles('client/api/measurement.js');
-
-    // Export global functions
-    api.export('pixelSpacingAutorunCheck', 'client');
-    api.export('handleMeasurementAdded', 'client');
-    api.export('handleMeasurementModified', 'client');
-    api.export('handleMeasurementRemoved', 'client');
-    api.export('syncMeasurementAndToolData', 'client');
-    api.export('syncImageMeasurementAndToolData', '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');
-    api.export('convertToNonTarget', 'client');
-    api.export('convertNonTarget', 'client');
-    api.export('timepointAutoCheck', '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('TrialCriteriaTypes', 'client');
-
-    // Export collections spanning both client and server
-    api.export('AdditionalFindings', [ 'client', 'server' ]);
-    api.export('ImageMeasurements', [ 'client', 'server' ]);
-    api.export('Measurements', [ 'client', 'server' ]);
-    api.export('Studies', [ 'client', 'server' ]);
-    api.export('Timepoints', [ 'client', 'server' ]);
-    api.export('Reviewers', [ 'client', 'server' ]);
-
-    // Export utility classes
-    api.export('FormUtils', 'client');
-});

Packages/lesiontracker/server/methods.js

@@ -1,61 +0,0 @@
-Meteor.methods({
-    removeMeasurement: function(id) {
-        var lesionData = Measurements.findOne(id);
-
-        // Update all Measurements to decrement the lesion numbers for those
-        // that were created after the current lesion by 1
-
-        // TODO: Update this when we have more criteria than patientId
-        // Decrement the absolute lesion number of all lesions with
-        // absolute lesion numbers greater than the current lesion by 1
-        Measurements.update({
-            patientId: lesionData.patientId,
-            lesionNumberAbsolute: {
-                $gt: lesionData.lesionNumberAbsolute
-            }
-        }, {
-            $inc: {
-                lesionNumberAbsolute: -1
-            }
-        }, {
-            multi: true
-        });
-
-        // Decrement the lesion number of all related (i.e. target or non-target)
-        // lesions with lesion numbers greater than the current lesion by 1
-        Measurements.update({
-            patientId: lesionData.patientId,
-            lesionNumber: {
-                $gt: lesionData.lesionNumber
-            },
-            isTarget: lesionData.isTarget
-        }, {
-            $inc: {
-                lesionNumber: -1
-            }
-        }, {
-            multi: true
-        });
-
-        Measurements.remove(id);
-    },
-    removeMeasurementsByPatientId: function(patientId) {
-        Measurements.remove({
-            patientId: patientId
-        });
-    },
-    removeImageMeasurementsByPatientId: function(patientId) {
-        ImageMeasurements.remove({
-            patientId: patientId
-        });
-    },
-    clearAllTimepoints: function() {
-        Timepoints.remove({});
-    },
-    removeTimepoint: function(id) {
-        Timepoints.remove(id);
-    },
-    removeAssociatedStudy: function(id) {
-        Studies.remove(id);
-    }
-});

Packages/ohif-cornerstone/client/cornerstoneTools.js

@@ -1,4 +1,4 @@
-/*! cornerstoneTools - v0.7.8 - 2016-08-05 | (c) 2014 Chris Hafey | https://github.com/chafey/cornerstoneTools */
+/*! cornerstoneTools - v0.7.9 - 2016-09-18 | (c) 2014 Chris Hafey | https://github.com/chafey/cornerstoneTools */
 // Begin Source: src/header.js
 if (typeof cornerstone === 'undefined') {
     cornerstone = {};
@@ -22,39 +22,64 @@ if (typeof cornerstoneTools === 'undefined') {
 
     'use strict';
 
+    var scrollTimeout;
+    var scrollTimeoutDelay = 1;
+
     function mouseWheel(e) {
-        // !!!HACK/NOTE/WARNING!!!
+        clearTimeout(scrollTimeout);
-        // for some reason I am getting mousewheel and DOMMouseScroll events on my
-        // mac os x mavericks system when middle mouse button dragging.
-        // I couldn't find any info about this so this might break other systems
-        // webkit hack
-        if (e.originalEvent.type === 'mousewheel' && e.originalEvent.wheelDeltaY === 0) {
-            return;
-        }
-        // firefox hack
-        if (e.originalEvent.type === 'DOMMouseScroll' && e.originalEvent.axis === 1) {
-            return;
-        }
 
-        var element = e.currentTarget;
+        scrollTimeout = setTimeout(function() {
-        var startingCoords = cornerstone.pageToPixel(element, e.pageX || e.originalEvent.pageX, e.pageY || e.originalEvent.pageY);
+            // !!!HACK/NOTE/WARNING!!!
+            // for some reason I am getting mousewheel and DOMMouseScroll events on my
+            // mac os x mavericks system when middle mouse button dragging.
+            // I couldn't find any info about this so this might break other systems
+            // webkit hack
+            if (e.originalEvent.type === 'mousewheel' && e.originalEvent.wheelDeltaY === 0) {
+                return;
+            }
+            // firefox hack
+            if (e.originalEvent.type === 'DOMMouseScroll' && e.originalEvent.axis === 1) {
+                return;
+            }
 
-        e = window.event || e; // old IE support
+            var element = e.currentTarget;
-        var wheelDelta = e.wheelDelta || -e.detail || -e.originalEvent.detail;
-        var direction = Math.max(-1, Math.min(1, (wheelDelta)));
 
-        var mouseWheelData = {
+            var x;
-            element: element,
+            var y;
-            viewport: cornerstone.getViewport(element),
-            image: cornerstone.getEnabledElement(element).image,
-            direction: direction,
-            pageX: e.pageX || e.originalEvent.pageX,
-            pageY: e.pageY || e.originalEvent.pageY,
-            imageX: startingCoords.x,
-            imageY: startingCoords.y
-        };
 
-        $(element).trigger('CornerstoneToolsMouseWheel', mouseWheelData);
+            if (e.pageX !== undefined && e.pageY !== undefined) {
+                x = e.pageX;
+                y = e.pageY;
+            } else if (e.originalEvent &&
+                       e.originalEvent.pageX !== undefined &&
+                       e.originalEvent.pageY !== undefined) {
+                x = e.originalEvent.pageX;
+                y = e.originalEvent.pageY;
+            } else {
+                // IE9 & IE10
+                x = e.x;
+                y = e.y;
+            }
+
+            var startingCoords = cornerstone.pageToPixel(element, x, y);
+
+            e = window.event || e; // old IE support
+            var wheelDelta = e.wheelDelta || -e.detail || -e.originalEvent.detail || -e.originalEvent.deltaY;
+            var direction = Math.max(-1, Math.min(1, (wheelDelta)));
+
+            var mouseWheelData = {
+                element: element,
+                viewport: cornerstone.getViewport(element),
+                image: cornerstone.getEnabledElement(element).image,
+                direction: direction,
+                pageX: x,
+                pageY: y,
+                imageX: startingCoords.x,
+                imageY: startingCoords.y
+            };
+
+            $(element).trigger('CornerstoneToolsMouseWheel', mouseWheelData);
+        }, scrollTimeoutDelay);
     }
 
     var mouseWheelEvents = 'mousewheel DOMMouseScroll';
@@ -798,6 +823,7 @@ if (typeof cornerstoneTools === 'undefined') {
         // we want to detect both the same time
         pinch.recognizeWith(pan);
         pinch.recognizeWith(rotate);
+        rotate.recognizeWith(pan);
 
         var doubleTap = new Hammer.Tap({
             event: 'doubletap',
@@ -2113,6 +2139,7 @@ if (typeof cornerstoneTools === 'undefined') {
             $(mouseEventData.element).on('CornerstoneToolsMouseMove', eventData, cornerstoneTools.arrowAnnotate.mouseMoveCallback);
             $(mouseEventData.element).on('CornerstoneToolsMouseDown', eventData, cornerstoneTools.arrowAnnotate.mouseDownCallback);
             $(mouseEventData.element).on('CornerstoneToolsMouseDownActivate', eventData, cornerstoneTools.arrowAnnotate.mouseDownActivateCallback);
+            $(mouseEventData.element).on('CornerstoneToolsMouseDoubleClick', eventData, cornerstoneTools.arrowAnnotate.mouseDoubleClickCallback);
         }
         
         // associate this data with this imageId so we can render it and manipulate it
@@ -2123,6 +2150,7 @@ if (typeof cornerstoneTools === 'undefined') {
         $(mouseEventData.element).off('CornerstoneToolsMouseMove', cornerstoneTools.arrowAnnotate.mouseMoveCallback);
         $(mouseEventData.element).off('CornerstoneToolsMouseDown', cornerstoneTools.arrowAnnotate.mouseDownCallback);
         $(mouseEventData.element).off('CornerstoneToolsMouseDownActivate', cornerstoneTools.arrowAnnotate.mouseDownActivateCallback);
+        $(mouseEventData.element).off('CornerstoneToolsMouseDoubleClick', cornerstoneTools.arrowAnnotate.mouseDoubleClickCallback);
 
         cornerstone.updateImage(mouseEventData.element);
         cornerstoneTools.moveNewHandle(mouseEventData, toolType, measurementData, measurementData.handles.end, function() {
@@ -3295,6 +3323,14 @@ if (typeof cornerstoneTools === 'undefined') {
 
                 // Set the invalidated flag to false so that this data won't automatically be recalculated
                 data.invalidated = false;
+
+                var eventType = 'CornerstoneToolsMeasurementModified';
+                var modifiedEventData = {
+                    toolType: toolType,
+                    element: element,
+                    measurementData: data
+                };
+                $(element).trigger(eventType, modifiedEventData);
             }
 
             // Define an array to store the rows of text for the textbox
@@ -3386,7 +3422,7 @@ if (typeof cornerstoneTools === 'undefined') {
                 };
 
                 // First we calculate the ellipse points (top, left, right, and bottom)
-                var ellipsePoints = [{
+                var ellipsePoints = [ {
                     // Top middle point of ellipse
                     x: leftCanvas + widthCanvas / 2,
                     y: topCanvas
@@ -3402,14 +3438,14 @@ if (typeof cornerstoneTools === 'undefined') {
                     // Right middle point of ellipse
                     x: leftCanvas + widthCanvas,
                     y: topCanvas + heightCanvas / 2
-                }];
+                } ];
 
                 // We obtain the link starting point by finding the closest point on the ellipse to the
                 // center of the textbox
                 link.start = cornerstoneMath.point.findClosestPoint(ellipsePoints, link.end);
 
                 // Next we calculate the corners of the textbox bounding box
-                var boundingBoxPoints = [{
+                var boundingBoxPoints = [ {
                     // Top middle point of bounding box
                     x: boundingBox.left + boundingBox.width / 2,
                     y: boundingBox.top
@@ -3435,7 +3471,7 @@ if (typeof cornerstoneTools === 'undefined') {
                 context.beginPath();
                 context.strokeStyle = color;
                 context.lineWidth = lineWidth;
-                context.setLineDash([2, 3]);
+                context.setLineDash([ 2, 3 ]);
                 context.moveTo(link.start.x, link.start.y);
                 context.lineTo(link.end.x, link.end.y);
                 context.stroke();
@@ -3461,6 +3497,7 @@ if (typeof cornerstoneTools === 'undefined') {
     });
 
 })($, cornerstone, cornerstoneMath, cornerstoneTools);
+ 
 // End Source; src/imageTools/ellipticalRoi.js
 
 // Begin Source: src/imageTools/freehand.js
@@ -4325,6 +4362,7 @@ if (typeof cornerstoneTools === 'undefined') {
     function mouseUpCallback(e, eventData) {
         $(eventData.element).off('CornerstoneToolsMouseDrag', dragCallback);
         $(eventData.element).off('CornerstoneToolsMouseUp', mouseUpCallback);
+        $(eventData.element).off('CornerstoneToolsMouseClick', mouseUpCallback);
         hideTool(eventData);
     }
 
@@ -4339,6 +4377,7 @@ if (typeof cornerstoneTools === 'undefined') {
         if (cornerstoneTools.isMouseButtonEnabled(eventData.which, e.data.mouseButtonMask)) {
             $(eventData.element).on('CornerstoneToolsMouseDrag', eventData, dragCallback);
             $(eventData.element).on('CornerstoneToolsMouseUp', eventData, mouseUpCallback);
+            $(eventData.element).on('CornerstoneToolsMouseClick', eventData, mouseUpCallback);
             drawMagnificationTool(eventData);
             return false; // false = causes jquery to preventDefault() and stopPropagation() this event
         }
@@ -4975,12 +5014,20 @@ if (typeof cornerstoneTools === 'undefined') {
         var lineWidth = cornerstoneTools.toolStyle.getToolWidth();
         var font = cornerstoneTools.textStyle.getFont();
         var fontHeight = cornerstoneTools.textStyle.getFontSize();
+        var config = cornerstoneTools.rectangleRoi.getConfiguration();
         
         for (var i = 0; i < toolData.data.length; i++) {
             context.save();
 
             var data = toolData.data[i];
             
+            // Apply any shadow settings defined in the tool configuration
+            if (config && config.shadow) {
+                context.shadowColor = config.shadowColor || '#000000';
+                context.shadowOffsetX = config.shadowOffsetX || 1;
+                context.shadowOffsetY = config.shadowOffsetY || 1;
+            }
+            
             //differentiate the color of activation tool
             if (data.active) {
                 color = cornerstoneTools.toolColors.getActiveColor();
@@ -5606,7 +5653,8 @@ if (typeof cornerstoneTools === 'undefined') {
                     x: mouseEventData.currentPoints.image.x,
                     y: mouseEventData.currentPoints.image.y,
                     highlight: true,
-                    active: true
+                    active: true,
+                    hasBoundingBox: true
                 }
             }
         };
@@ -5655,12 +5703,13 @@ if (typeof cornerstoneTools === 'undefined') {
 
     ///////// BEGIN IMAGE RENDERING ///////
     function pointNearTool(element, data, coords) {
-        if (!data.textBoundingBox) {
+        if (!data.handles.end.boundingBox) {
             return;
         }
 
-        var distanceToPoint = cornerstoneMath.rect.distanceToPoint(data.textBoundingBox, coords);
+        var distanceToPoint = cornerstoneMath.rect.distanceToPoint(data.handles.end.boundingBox, coords);
-        return (distanceToPoint < 10);
+        var insideBoundingBox = cornerstoneTools.pointInsideBoundingBox(data.handles.end, coords);
+        return (distanceToPoint < 10) || insideBoundingBox;
     }
 
     function onImageRendered(e, eventData) {
@@ -5707,7 +5756,7 @@ if (typeof cornerstoneTools === 'undefined') {
             };
 
             var boundingBox = cornerstoneTools.drawTextBox(context, data.text, textCoords.x, textCoords.y - 10, color, options);
-            data.textBoundingBox = boundingBox;
+            data.handles.end.boundingBox = boundingBox;
 
             context.restore();
         }
@@ -8423,7 +8472,7 @@ Display scroll progress bar across bottom of image.
         // When the user has scrolled to a new image
         clearTimeout(resetPrefetchTimeout);
         resetPrefetchTimeout = setTimeout(function() {
-            var element = e.currentTarget;
+            var element = e.target;
             prefetch(element);
         }, resetPrefetchDelay);
     }