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

PETSUVMeasurements/client/body.styl

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+body
+  background-color: black

PETSUVMeasurements/client/components/app/app.html

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+<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

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+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

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+@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

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+<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

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+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

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+@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

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+<template name="viewer">
+    {{#if Template.subscriptionsReady}}
+        <div class="viewerDialogs">
+            {{>confirmDeleteDialog}}
+            {{>measurementTableHUD (clone this)}}
+        </div>
+        <div id="viewer">
+            {{>toolbarSection (clone this)}}
+            {{>viewerSection (clone this)}}
+        </div>
+    {{else}}
+        {{>loadingText}}
+    {{/if}}
+</template>

PETSUVMeasurements/client/components/viewer/viewer.js

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+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

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+@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

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+<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

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+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

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+@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

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+<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

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+// 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']
+});