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index.html
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<!DOCTYPE html>
<html>
<head>
<title> SMARTer </title>
<link rel="stylesheet" href="lib/css/bootstrap.min.css">
<link rel="stylesheet" href="lib/css/d3-tip.css">
<link rel="stylesheet" href="lib/css/phoneLayout.css">
<link rel="stylesheet" href="lib/css/tabletLayout.css">
<link rel="stylesheet" href="lib/css/laptopLayout.css">
<link rel="stylesheet" href="lib/css/controls.css">
<!-- <link rel="stylesheet" href="https://rawgithub.com/Caged/d3-tip/master/examples/example-styles.css"> -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
<!-- bootstrap select -->
<!-- <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css"> -->
<link rel="stylesheet" href="lib/css/bootstrap-select.css">
<!-- <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script> -->
<!-- <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script> -->
<link rel="stylesheet/less" href="src/css/style.less">
<link rel="stylesheet/less" href="src/css/kiviat.less">
<link rel="stylesheet/less" href="src/css/nomogram.less">
<link rel="stylesheet/less" href="src/css/mosaic.less">
<link rel="stylesheet/less" href="src/css/kaplanMeier.less">
<script src="https://cdnjs.cloudflare.com/ajax/libs/less.js/2.7.2/less.min.js" charset="utf-8"></script>
<!-- MATH library -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjs/7.0.0/math.min.js"></script>
<!-- axios -->
<script src="https://cdn.jsdelivr.net/npm/axios/dist/axios.min.js"></script>
<script src="https://unpkg.com/axios/dist/axios.min.js"></script>
<script src="lib/js/d3.v4.min.js" charset="utf-8"></script>
<script src="lib/js/jquery.min.js" charset="utf-8"></script>
<script src="lib/js/bootstrap.min.js" charset="utf-8"></script>
<!-- <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script> -->
<!-- bootsrap select -->
<script src="lib/js/bootstrap-select.js"></script>
<script src="lib/js/lodash.min.js" charset="utf-8"></script>
<script src="lib/js/d3.nomogram.js"></script>
<script src="lib/js/d3-tip.js" charset="utf-8"></script>
<!-- regression libraries -->
<!-- <script src="lib/js/jsregression.js"></script> -->
<!-- <script src="lib/js/regression.js"></script> -->
<!-- <script src="https://www.lactame.com/lib/ml/2.2.0/ml.min.js"></script> -->
<script src="src/js/model/patientModel.js" charset="utf-8"></script>
<script src="src/js/model/applicationStateModel.js" charset="utf-8"></script>
<script src="src/js/model/kaplanMeierPatientModel.js" charset="utf-8"></script>
<script src="src/js/model/axesModel.js" charset="utf-8"></script>
<script src="src/js/model/attributeModel.js" charset="utf-8"></script>
<!-- for predictive analysis -->
<!-- <script src="src/js/model/logisticRegression.js" charset="utf-8"></script> -->
<!-- <script src="src/js/model/predictiveAnalysis.js"></script> -->
<!-- <script src="src/js/model/R_predictive_data.js"></script> -->
<script src="src/js/controller/dataUpdateController.js" charset="utf-8"></script>
<script src="src/js/controller/patientSelectorController.js" charset="utf-8"></script>
<script src="src/js/controller/attributeSelectorController.js" charset="utf-8"></script>
<!-- <script src="src/js/controller/attributeSelectorControllerUpdated.js"></script> -->
<script src="src/js/controller/nomogramKnnController.js" charset="utf-8"></script>
<script src="src/js/controller/filterController.js" charset="utf-8"></script>
<script src="src/js/controller/exploreFormController.js" charset="utf-8"></script>
<script src="src/js/controller/addPatientController.js" charset="utf-8"></script>
<script src="src/js/controller/knnAttributeSelectionController.js" charset="utf-8"></script>
<script src="src/js/controller/kiviatAttributeSelectionController.js" charset="utf-8"></script>
<script src="src/js/controller/nomogramAxisController.js" charset="utf-8"></script>
<script src="src/js/controller/settingsController.js" charset="utf-8"></script>
<script src="src/js/controller/LandingFormController.js" charset="utf-8"></script>
<script src="src/js/controller/kaplanMeierCheckboxController.js" charset="utf-8"></script>
<script src="src/js/controller/nomogramPredictInfoController.js" charset="utf-8"></script>
<!-- add new patient -->
<script src="src/js/controller/addNewPatient.js" charset="utf-8"></script>
<script src="src/js/view/kiviatDiagramView.js" charset="utf-8"></script>
<script src="src/js/view/nomogramView.js" charset="utf-8"></script>
<script src="src/js/view/kaplanMeierView.js" charset="utf-8"></script>
<script src="src/js/view/statsView.js" charset="utf-8"></script>
<!-- <script src="src/js/view/helpInfoView.js" charset="utf-8"></script> -->
<script src="src/js/view/demographicsFormView.js" charset="utf-8"></script>
<script src="src/js/view/treatmentFormView.js" charset="utf-8"></script>
<script src="src/js/view/cancerDescriptorsFormView.js" charset="utf-8"></script>
<script src="src/js/view/statisticsModalView.js" charset="utf-8"></script>
<!-- <script src="src/js/view/predictiveProbabilityView.js" charset="utf-8"></script> -->
<script src="src/js/view/predictionAttributeModal.js" charset="utf-8"></script>
<script src="src/js/view/radiomicView.js" charset="utf-8"></script>
<script src="src/js/main.js" charset="utf-8"></script>
</head>
<body>
<div id="loading">
<img id="loading-image" src="imgs/loading.gif" alt="Loading..." />
</div>
<!-- home page starts -->
<div class="container-fluid landing-form align-top">
<h3 class=title>SMART Therapy Explorer</h3>
<div class="row">
<div class="col-xs-12 col-sm-6 col-md-4 col-lg-4">
<button type="button" class="demoButton" data-toggle="collapse" data-target="#demographics">Demographics <sup><i class="fa fa-asterisk" style="color: whites;"></i></sup></button>
<div id="demographics" class="collapse">
<label>Patient ID</label>
<select class="idSelect">
<option>N/A</option>
</select>
<label id="age-label"><span>Age<sup><i class="fa fa-asterisk" id="age-validation"></i></sup></span></label>
<input type="text" name="Age at Diagnosis (Calculated)" id="age-element" placeholder="Age">
<!-- <div id="age-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide Age</div> -->
<label id="gender-label"><span>Gender<sup><i class="fa fa-asterisk" id="gender-validation"></i></sup></span></label>
<input type="radio" name="Gender" value="Male" id="male-radio">Male
<input type="radio" name="Gender" value="Female" id="female-radio">Female
<!-- <div id="gender-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide Gender</div> -->
<label>Race</label>
<select id="race-element" name="Race">
<!-- <option value="" disabled selected>Race </option> -->
<option value="White/Caucasion">White/Caucasion</option>
<option value="Other">Other</option>
<option value="N/A" selected>N/A</option>
</select>
<!-- <div id="race-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide Race</div> -->
<!-- <input type="text" name="Race" placeholder="Race" id="race-element"> -->
<label>Aspiration</label>
<input type="radio" name="Aspiration rate Pre-therapy" value="Y" id="aspiration-y-radio">Yes
<input type="radio" name="Aspiration rate Pre-therapy" value="N" id="aspiration-n-radio">No
<input type="radio" name="Aspiration rate Pre-therapy" value="N/A" id="aspiration-na-radio" checked>N/A
<!-- <div id="aspiration-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide Aspiration</div> -->
<!-- <input type="text" name="HPV/P16 status" placeholder="HPV/P16" id="hpvp16-element"> -->
<label id="smoking-label"><span>Smoking Status<sup><i class="fa fa-asterisk" id="smoking-validation"></i></sup></span></label>
<input type="radio" name="Smoking status at Diagnosis (Never/Former/Current)" value="Never" id="smoking-never-radio">Never
<input type="radio" name="Smoking status at Diagnosis (Never/Former/Current)" value="Former" id="smoking-former-radio">Former
<input type="radio" name="Smoking status at Diagnosis (Never/Former/Current)" value="Current" id="smoking-current-radio">Current
<!-- <div id="smoking-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide Smoking Status</div> -->
<label>Packs/Year</label>
<input type="text" name="Smoking status (Packs/Year)" placeholder="Packs Per Year" id="packs-per-year-element">
<!-- <div id="packs-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide Packs/Year</div> -->
<div>
<button class="btn btn-primary" type="button" data-toggle="collapse" data-target="#demographics">Next</button>
</div>
</div>
</div>
<div class="col-xs-12 col-sm-6 col-md-4">
<button type="button" id="cancer" class="cancerButton" data-toggle="collapse" data-target="#cancerDescriptors">Cancer Descriptors <sup><i class="fa fa-asterisk" style="color: white;"></i></sup></button>
<div id="cancerDescriptors" class="collapse">
<label>Tm Laterality (R/L)</label>
<select id="tumor-site" name="Tm Laterality (R/L)">
<option value="" disabled selected>R/L/Bilateral</option>
<option value="R">R</option>
<option value="L">L</option>
<option value="Bilateral">Bilateral</option>
<option value="N/A" selected>N/A</option>
</select>
<!-- <div id="site-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide Tm Laterality</div> -->
<!-- <input type="text" name="Tm Laterality (R/L)" placeholder="R/L/Bilateral" id="tumor-site"> -->
<label>Tumor Subsite</label>
<select id="tumor-subsite" name="Tumor subsite (BOT/Tonsil/Soft Palate/Pharyngeal wall/GPS/NOS)">
<option value="" disabled selected>Tumor Subsite</option>
<option value="BOT">BOT</option>
<option value="Tonsil">Tonsil</option>
<option value="Other" selected>Other</option>
</select>
<!-- <div id="subsite-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide Tumor Subsite</div> -->
<label>HPV/P16</label>
<select id="hpvp16-element" name="HPV/P16 status">
<option value="" disabled selected>HPV/P16</option>
<option value="Positive">Positive</option>
<option value="Negative">Negative</option>
<option value="Unknown" selected>Unknown</option>
</select>
<!-- <div id="hpvp16-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide HPV/P16</div> -->
<!-- <input type="text" name="Tumor subsite (BOT/Tonsil/Soft Palate/Pharyngeal wall/GPS/NOS)" placeholder="Tumor Subsite" id="tumor-subsite"> -->
<!-- <label>AJCC 7th Edition</label>
<input type="radio" name="AJCC 7th edition" value="I" id="ajcc7-1">I
<input type="radio" name="AJCC 7th edition" value="II" id="ajcc7-2">II
<input type="radio" name="AJCC 7th edition" value="III" id="ajcc7-3">III
<input type="radio" name="AJCC 7th edition" value="IV" id="ajcc7-4">IV
<label>AJCC 8th Edition</label>
<input type="radio" name="AJCC 8th edition" value="I" id="ajcc8-1">I
<input type="radio" name="AJCC 8th edition" value="II" id="ajcc8-2">II
<input type="radio" name="AJCC 8th edition" value="III" id="ajcc8-3">III
<input type="radio" name="AJCC 8th edition" value="IV" id="ajcc8-4">IV -->
<label id="tcat-label"><span>T-category<sup><i class="fa fa-asterisk" id="t-validation"></i></sup></span></label>
<input type="radio" name="T-category" value="T1" id="tcat1">T1
<input type="radio" name="T-category" value="T2" id="tcat2">T2
<input type="radio" name="T-category" value="T3" id="tcat3">T3
<input type="radio" name="T-category" value="T4" id="tcat4">T4
<!-- <div id="t-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide T-Category</div> -->
<label id="ncat-label"><span>N-Category<sup><i class="fa fa-asterisk" id="n-validation"></i></sup></span></label>
<!-- <input type="radio" name="N-category" value="N/A" id="ncat-na">N/A -->
<input type="radio" name="N-category" value="N0" id="ncat-0">N0
<input type="radio" name="N-category" value="N1" id="ncat-1">N1
<input type="radio" name="N-category" value="N2" id="ncat-2">N2
<input type="radio" name="N-category" value="N3" id="ncat-3">N3
<!-- <div id="n-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide N-Category</div> -->
<label>Pathological Grade</label>
<input type="radio" name="Pathological Grade" value="I" id="pgrade1">I
<input type="radio" name="Pathological Grade" value="II" id="pgrade2">II
<input type="radio" name="Pathological Grade" value="III" id="pgrade3">III
<input type="radio" name="Pathological Grade" value="IV" id="pgrade4">IV
<input type="radio" name="Pathological Grade" value="N/A" id="pgradeNA" checked>N/A
<!-- <div id="pathological-validation" style="color: red;"><sup><i class="fa fa-asterisk"></i></sup>Please, Provide Pathological Grade</div> -->
<label>Affected Lymph Nodes</label>
<input type="text" name="Affected Lymph node" placeholder="Affected Lymph Node" id="affected-lymph">
<div>
<button class="btn btn-primary" type="button" data-toggle="collapse" data-target="#cancerDescriptors">Next</button>
</div>
</div>
</div>
<div class="col-xs-12 col-sm-12 col-md-4 col-lg-4">
<button type="button" class="treatmentButton" data-toggle="collapse" data-target="#treatment">Treatment (If Any)</button>
<div id="treatment" class="collapse">
<div class="left">
<label>Chemotherapy</label>
<select id="chemo-element" name="Therapeutic combination">
<!-- <option value="" disabled selected>Therapeutic combination</option> -->
<option value="CC">CC</option>
<option value="IC+CC">IC+CC</option>
<option value="IC+Radiation alone">IC+Radiation alone</option>
<option value="Radiation alone">Radiation alone</option>
<option value="N/A" selected>N/A</option>
</select>
<!-- <input type="text" name="Therapeutic combination" placeholder="Therapeutic combination" id="chemo-element"> -->
<!-- <label>Censor</label> -->
<!-- <input type="text" name="Censor" placeholder="0/1" id="local-therapy-element"> -->
<label>Treatment Duration</label>
<input type="text" name="Treatment duration (Days)" placeholder="Duration" id="duration-element">
<label>Total Dose</label>
<input type="text" name="Total dose" placeholder="Total Dose" id="total-dose-element">
</div>
<div class="right">
<label>Total Fraction</label>
<input type="text" name="Total fractions" placeholder="Total Fraction" id="total-fraction-element">
<label>Dose/Day</label>
<input type="text" name="Dose/fraction (Gy)" placeholder="Dose Per Day" id="dose-element">
<label>Neck Dissection after IMRT</label>
<input type="radio" name="Neck Disssection after IMRT (Y/N)" value="Y" id="neck-dissect-y-radio">Yes
<input type="radio" name="Neck Disssection after IMRT (Y/N)" value="N" id="neck-dissect-n-radio">No
<input type="radio" name="Neck Disssection after IMRT (Y/N)" value="N/A" id="neck-dissect-n/a-radio" checked>N/A
<!-- <input type="text" name="Neck Disssection after IMRT (Y/N)" placeholder="Neck Dissection" id="neck-dissection-element"> -->
<label>Neck Boost</label>
<input type="radio" name="Neck boost (Y/N)" value="Y" id="neck-boost-y-radio">Yes
<input type="radio" name="Neck boost (Y/N)" value="N" id="neck-boost-n-radio">No
<input type="radio" name="Neck boost (Y/N)" value="N/A" id="neck-boost-n/a-radio" checked>N/A
</div>
</div>
</div>
</div>
<button class="btn btn-primary submitButton" type="submit" value="Submit">Submit</button>
</div>
<!-- home page ends -->
<!-- help menu i suppose -->
<div class="info-overlay dashboard-help">
<img id="helpImg" src="imgs/help.png">
</div>
<div class="container-fluid dashboard align-top">
<!-- navigation bar on the top -->
<div class="row" id="title">
<!-- <nav class="navbar"> -->
<div class="container-fluid navbar-grey">
<div class="col-md-5"> <!-- navbar-header"> -->
<a href="#">SMARTer Therapy Explorer</a> <!-- class="navbar-brand"-->
<button type="button" class="btn btn-default btn-sm" id= "statButton" data-toggle="modal" data-target="#exampleModal">
Statistics
</button>
<button type="button" class="btn btn-default btn-sm" id= "cohortButton" data-toggle="modal" data-target="#cohortModal">
Cohort
</button>
<button class="btn btn-default navbar-btn" id="add-patient-button">
<span class="glyphicon glyphicon-plus"></span>
Update Patient
</button>
</div>
<!-- patient dropdown menu -->
<div class="col-md-4 patient-dropdown-wrapper" id="similarPatientList" style="text-align: left; padding-left: 3%;">
<div class="col-md-6 form-inline" style="padding-right: 0; padding-left: 6%;">
<div class="form-group">
<label for="patientSel">Patient ID:</label>
<select class="patient-dropdown form-control input-sm" id="patientSel"></select>
</div>
</div>
<div class="col-md-6" id="subjectPrediction" style="padding-left: 0; padding-right: 0;"></div>
</div>
<div class="col-md-3">
<ul class="nav navbar-nav navbar-right">
<button class="btn btn-link navbar-btn" data-toggle="modal" data-target="#aboutModal">
<span class="glyphicon glyphicon-info-sign"></span>
About
</button>
<button type="button" class="btn btn-link navbar-btn" id="HelpInfo" data-toggle="modal" data-target="#OverallHelpInfo">
<span class="glyphicon glyphicon-question-sign"></span>
Help
</button>
</ul>
</div>
</div>
<!-- </nav> -->
</div>
<!-- nav bar ends -->
<div class="row" id="allContent">
<div class="row" id="top">
<div class="col-md-3">
<!-- kaplan meier plot -->
<!-- <div class="row" id="kaplanTop"> -->
<div class="col contentWrapper kaplanDiv">
<div class="contentDiv">
<div class="infoDiv" id="infoDiv-kaplanMeier">
</div>
<div id="kaplanMeierHeader">
<div class="row viewTitleDiv">
Survival Over Time
<!-- Button trigger modal -->
<!-- <button type="button" class="btn btn-primary" data-toggle="modal" data-target="#kaplanmeierModal"> -->
<span class="glyphicon glyphicon-question-sign" data-toggle="modal" data-target="#kaplanmeierModal" id="HelpInfo-kaplanMeier"></span>
<!-- </button> -->
</div>
<div class="row patient-dropdown-wrapper">
<div class="col-md-8" id="updated_dropdown">
</div>
<!-- <div class="col-md-4" style="font-size: 12px;">
<input id="kmcheckbox" type="checkbox" style="display:inline" checked> KM Estimator
</div> -->
</div>
</div>
<div id="kaplanMeier">
</div>
</div>
</div>
<!-- </div> -->
</div>
<!-- right divided int nomogram on top
and kaplan meier and the table on botom -->
<div class="col-md-7" id="right">
<!-- <div class="row"> -->
<!-- <div class="col-md-12 contentWrapper nomogramDiv"> -->
<div class="contentDiv">
<!-- <div class="infoDiv" id="infoDiv-nomogram">
</div> -->
<!-- just the title and stuffs -->
<div id="nomogramHeader">
<div class="row viewTitleDiv">
Survival and Toxicity Risk Prediction
<!-- Button trigger modal -->
<!-- <button type="button" class="btn btn-primary" data-toggle="modal" data-target="#nomogramModal"> -->
<span class="glyphicon glyphicon-question-sign" data-toggle="modal" data-target="#nomogramModal" id="HelpInfo-nomogram"></span>
<!-- </button> -->
</div>
<div class="row">
<div class="col-md-4" id="polylineLegend" style="top: 30px;">
</div>
<div class="col-md-4 col-md-4" style="bottom: 10px;width: 28%;">
<select class="btn btn-outline btn-grey btn-block dropdown-toggle" id="nomogram-selector"></select>
</div>
<div class="col-md-4 knnCheckBox" style="bottom: 10px; left: 16%;">
<input id="knnCheckBox" type="checkbox" style="display:inline" checked> Show K-Nearest Neighbors</input>
</div>
</div>
<!-- <div class="row knnCheckBox">
<input id="knnCheckBox" type="checkbox" style="display:inline" checked> Show K-Nearest Neighbors</input>
</div> -->
</div>
<div id="nomogram">
</div>
</div>
<!-- </div> -->
<!-- </div> -->
</div>
<div class="col-md-2 contentWrapper controlDiv" style="display: block" id="unbelievable-fix">
<div class="row">
<div class="col-md-4" style="padding-top: 30%;">
<!-- <div class= "row" id="subjectPrediction"></div> -->
<div class="row">
<label style="text-align: center;">Prediction With Radiomics
<span class="glyphicon glyphicon-question-sign" data-toggle="modal" data-target="#WithRadiomics"></span>
</label>
<div id="radiomicLegend"></div>
<!-- <select id="radiomic_dropdown" name="radiomic"> -->
<!-- <option value="" disabled selected>Race </option> -->
<!-- <option value="Cluster1">Cluster 1</option>
<option value="Cluster2">Cluster 2</option>
<option value="Cluster3">Cluster 3</option> -->
<!-- </select> -->
</div>
<div class="row" id="withLymphnode"></div>
</div>
<div class="col-md-8" id="radiomics"></div>
</div>
</div>
<!-- nomogram control box -->
<div class="col-md-2 contentWrapper controlDiv nomogramControlsBox">
<div class="infoDiv" id="infoDiv-nomogramControls">
</div>
<div class="contentDiv" id="nomogramControls">
<div class="row dropdown-control-row">
<h5>
Nomogram Controls
</h5>
<!-- first dropdown menu -->
<div class="col-md-12">
<div class="row dropdown-row">
<div class="dropdown">
<button class="btn btn-default btn-block dropdown-toggle" type="button" data-toggle="dropdown">
<span class="glyphicon glyphicon-eye-open"></span>
Nomogram Axis
<span class="caret"></span>
</button>
<ul class="dropdown-menu col-sm-12" id="nomogramVisibilityControl">
<!-- populating list in controller -->
</ul>
</div>
</div>
</div>
</div>
<div class="row axis-control-row">
<div class="col-md-10">
<div class="row">
<h5>Edit Axes:</h5>
<div class="form-group">
<label for="nomogramAxisSelect">Selected Axis:</label>
<select id="nomogramAxisSelect" class="form-control">
<!-- <option value="x">Option 1</option> -->
</select>
</div>
<div class="btn-group btn-group-justified">
<div class="btn-group">
<button type="button" class="btn btn-default btn-outline nomogramAxisButton" id="nomogramAxisDomainButton" value="domain" data-toggle="tooltip" title="Use the slider on the right">Domain</button>
</div>
<div class="btn-group">
<button type="button" class="btn btn-default btn-outline active nomogramAxisButton" id="nomogramAxisRangeButton" value="range" data-toggle="tooltip" title="Use the slider on the right">Range</button>
</div>
</div>
</div>
<div class="row" style="margin-top:10px;">
<button type="button" class="btn btn-outline btn-default" id="nomogramResetButton">Reset</button>
</div>
</div>
<div class="col-md-2 axisSliderWrapper">
<div id="axisHeightSlider">
</div>
</div>
</div>
</div>
</div>
</div>
<!-- <div class="row"> -->
<div class="row" id="bottom">
<div class="contentWrapper kiviatDiv">
<div class="contentDiv">
<!-- kiviat header - title and dropdown -->
<div class="viewTitleDiv" id="kiviatHeader">
<div class="col-md-4" style="padding-left: 18%;">
Current Patient
<!-- Button trigger modal -->
<!-- <button type="button" class="btn btn-primary" data-toggle="modal" data-target="#kiviatModal"> -->
<span class="glyphicon glyphicon-question-sign" data-toggle="modal" data-target="#kiviatModal" id="HelpInfo-kiviat"></span>
<!-- </button> -->
</div>
<!-- kiviat title -->
<div class="col-md-6" style="padding-left: 12%;">
Most Similar Patients
<!-- Button trigger modal -->
<!-- <button type="button" class="btn btn-primary" data-toggle="modal" data-target="#kiviatModal"> -->
<span class="glyphicon glyphicon-question-sign" data-toggle="modal" data-target="#kiviatModal" id="HelpInfo-kiviat"></span>
<!-- </button> -->
</div>
<div class="col-md-2 dropdown">
<button class="btn btn-default dropdown-toggle btn-sm" type="button" id="dropdownMenuButton" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<span class="glyphicon glyphicon-wrench" style="font-size: 12px;"></span>
</button>
<div class="dropdown-menu" id="kiviatDropdown" aria-labelledby="dropdownMenuButton" style="height: 55px; width: 345px;">
<!-- KNN controller -->
<button class="btn btn-default dropdown-toggle " type="button" data-toggle="collapse" data-target="#knnAttributesControl">
KNN Attributes Used
<span class="caret"></span>
</button>
<!-- kiviat axes controller -->
<button class="btn btn-default dropdown-toggle" type="button" data-toggle="collapse" data-target="#kiviatAttributesControl" >
Patient Axes Control
<span class="caret"></span>
</button>
</div>
</div>
</div>
<!-- kiviat diagram itself -->
<div id="kiviatDiagram">
<!-- divided into two
left one contains the subject's kiviat and legend
right one contains the matching kiviats -->
<div class="col-md-4 kiviatLeft">
<!-- patient dropdown menu -->
<!-- <div class="row patient-dropdown-wrapper" id="similarPatientList">
<div class="form-inline">
<div class="form-group">
<label for="patientSel">Patient:</label>
<select class="patient-dropdown form-control input-sm" id="patientSel"></select>
</div>
</div>
</div> -->
<div>
<!-- kiviat diagram legend -->
<div class="col-md-5" id="kiviatDiagram-legend">
</div>
<!-- subject's kiviat diagram -->
<div class="col-md-7" id="kiviatDiagram-subject">
</div>
</div>
</div>
<!-- neghbors kiviat diagram -->
<div class="col-md-8">
<div class="row">
<div class="col-md-6">
<!-- KNN controller -->
<!-- <button class="btn btn-default dropdown-toggle " type="button" data-toggle="collapse" data-target="#knnAttributesControl">
KNN Attributes Used
<span class="caret"></span>
</button> -->
<!-- <div class="col-md-3" style="height: 100%;"> -->
<ul class="dropdown-menu col-sm-12 col-md-4 optionDropdown scrollCollapse" id="knnAttributesControl">
<!-- populating list in controller -->
<!-- <div class="modal-footer">
<button class="btn btn-default dropdown-toggle" type="button" data-toggle="collapse" data-target="#knnAttributesControl">
Close
</button>
</div> -->
</ul>
<!-- </div> -->
</div>
<div class="col-md-6">
<!-- kiviat axes controller -->
<!-- <button class="btn btn-default dropdown-toggle" type="button" data-toggle="collapse" data-target="#kiviatAttributesControl" >
Patient Axes Control
<span class="caret"></span>
</button> -->
<ul class="dropdown-menu col-sm-12 col-md-4 scrollCollapse" id="kiviatAttributesControl">
<!-- populating list in controller -->
<!-- <div class="modal-footer">
<button class="btn btn-default dropdown-toggle" type="button" data-toggle="collapse" data-target="#kiviatAttributesControl" >
Close
</button>
</div> -->
</ul>
</div>
</div>
<div class="row">
<div class="col-md-12 kiviatRight" id="kiviatDiagram-neighbors"></div>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- </div> -->
</div>
</div>
<!-- cohort view modal -->
<div class="modal fade" id="cohortModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<!-- <h5 class="modal-title" id="exampleModalLabel">Statistics Of All Patients</h5> -->
<h3 class="modal-title">Cohort Distribution</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<table id="commonAttributesTable" class=" table order-list">
<thead>
<tr>
<td>Attribute</td>
<td>Same value knn patients</td>
</tr>
</thead>
<tbody>
<tr>
<td class="col-sm-6">
<span class="">Gender</span>
</td>
<td class="col-sm-6">
<span class="">5</span>
</td>
</tr>
</tbody>
<tfoot>
<!-- <tr>
<td colspan="5" style="text-align: left;">
</td>
</tr>
<tr>
</tr> -->
</tfoot>
</table>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- statistics modal -->
<!-- Modal -->
<div class="modal fade" id="exampleModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<!-- <h5 class="modal-title" id="exampleModalLabel">Statistics Of All Patients</h5> -->
<h3 class="modal-title">Statistics of All Patients</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body" id="statisticsModalBody">
<table class="table table-bordered statsTable">
<thead>
<tr>
<th scope="col">Attribute Name</th>
<th scope="col">Count/Mean</th>
</tr>
</thead>
<tbody>
<tr>
<td>Mark</td>
<td>Otto</td>
</tr>
<tr>
<td>Jacob</td>
<td>Thornton</td>
</tr>
<tr>
<td colspan="2">Larry the Bird</td>
</tr>
</tbody>
</table>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- help information modals -->
<!-- overall help modal -->
<!-- Modal -->
<div class="modal fade" id="OverallHelpInfo" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="exampleModalLabel">The SMART Therapy Explorer</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<ul>
<li><strong>About</strong> describes the project</li>
<li>Using the <strong>Update Patients</strong> button, patient’s info can be updated or new patient can be added</li>
<li>Clicking the <strong>Statistics</strong> button will show detailed statistics of all patients</li>
<li>Clicking the <strong>Cohort</strong> button will show the subgroup analysis of the selected patients</li>
<li><strong>Survival Over Time</strong> view in the left shows the probability of survival over time</li>
<li><strong>Survival and Toxicity Risk Prediction</strong> shows a graphical calculating device for Probability fo Survival</li>
<li><strong>Lymph Nodes Clusters</strong> button will show the Lymph Node Clusters Page</li>
<li>The Bottom Part shows patient attributes. The <strong>Current Patient</strong> view shows the attributes of the selected
patient and the <strong>Most Similar Patients</strong> view shows the attributes of patients that are most similar to the
selected patient</li>
<li>Clicking on the Question Marks (?) beside each view will show help information for that view</li>
</ul>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- kiviat diagram help modal -->
<!-- Modal -->
<div class="modal fade" id="kiviatModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title" id="exampleModalLabel">Current Patient and Most Similar Patients</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<ul>
<li>Select desired patient from the dropdown list <br> <br>
<img src="imgs/kiviat/select-dropdown.png" style="width: 50%; display: block; margin-left: auto; margin-right: auto;">
<br><br>
</li>
<li><strong>Current Patient</strong> view shows the current selected patient</li>
<li><strong>Most Similar Patients</strong> view shows five most similar patients for the selected patient</li>
<li>The views shows nine characteristics of the patient
<ul>
<li>Age</li>
<li>Gender</li>
<li>Race</li>
<li>T-Category</li>
<li>N-Category</li>
<li>Tumor Subsite</li>
<li>Therapeutic Combination</li>
<li>Smoking Status</li>
<li>HPV/P16</li>
</ul>
</li>
<li>The Color indicates probabilty of survival</li>
<li>Mouse Over to see details <br><br>
<div style="display:flex;">
<div style="flex: 50%; padding: 5px;">
<img src="imgs/kiviat/mouseOver.png" alt="mouse over" style="width:100%">
</div>
<div style="flex: 50%; padding: 5px;">
<img src="imgs/kiviat/mouseOverAxis.png" alt="mouse over axis" style="width:100%">
</div>
</div>
<!-- <img src="imgs/kiviat/mouseOver.png" style="width: 50%; display: inline-block; margin-left: auto; margin-right: auto;">
<img src="imgs/kiviat/mouseOverAxis.png" style="width: 50%; display: inline-block; margin-left: auto; margin-right: auto;"> -->
</li>
<li>For each similar patient, similarity score and different survival probability are shown beneath each view</li>
<li>Use the controll settings to select Attributes for calculating most similar patients (KNN Attributes Used)</li>
<li>Use the controll settings to see less or more patient axes (Patient Axes Control)</li>
</ul>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- nomogram help modal -->
<!-- Modal -->
<div class="modal fade" id="nomogramModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title" id="exampleModalLabel">Survival and Toxicity Risk Prediction</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<ul>
<li>Choose the desired prediction from the drop down menu <br><br>
<img src="imgs/nomogram/nomogram-dropdown.png" style="width: 100%; display: block; margin-left: auto; margin-right: auto;">
<br><br>
</li>
<li>Use the controller setting to control which scales and scale-intervals are shown. <br> <br>
<img src="imgs/nomogram/controller settings.PNG" style="width: 100%; display: block; margin-left: auto; margin-right: auto;">
<br><br>
</li>
<li>Use the controller setting to resize and reposition each axis <br><br>
<img src="imgs/nomogram/resize.PNG" style="width: 100%; display: block; margin-left: auto; margin-right: auto;">
<br><br>
</li>
<li>In the view, the thick dark polyline corresonds to the patient that the user selected.<br>
The remaining polylines correspond to the five most similar patients.</li>
<li>Mouse over a poly line to view that poly line only</li>
<li>Uncheck "Show K-Nearest Neighbors" to see all of the patients information</li>
<li>Click on the question mark (?) over "Predictive Probability" to view "Attributes Used in Predicting The Outcomes"</li>
</ul>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- kaplan meier help modal -->
<!-- Modal -->
<div class="modal fade" id="kaplanmeierModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title" id="exampleModalLabel">Survival Over Time</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<ul>
<li>Survival Over Time view showing survival over time per patient group,
depending on the selected attribute</li>
<li>From the dropdown, attributes can be selected <br><br>
<img src="imgs/kaplan/dropdown.jpg" style="width: 100%; display: block; margin-left: auto; margin-right: auto;">
</li>
<li>User can select to view all values or any particular value from the dropdown</li>
<li>By default, selected patient's (from patient ID dropdown) cohort color is more opaqued than the other cohorts</li>
<li>Mouse Over to the legends to view the cohort <br><br>
<img src="imgs/kaplan/legend.png" style="width: 100%; display: block; margin-left: auto; margin-right: auto;">
</li>
<li>Mouse Over the view to see details <br><br>
<img src="imgs/kaplan/mouseover.png" style="width: 100%; display: block; margin-left: auto; margin-right: auto;">
</li>
</ul>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- statistics and cohort help modal -->
<!-- Modal -->
<div class="modal fade" id="statHelpModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title" id="exampleModalLabel">Statisctics and Cohort</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<ul>
<li>The first row of the table shows how many similar patients are in the repository from the subgroup (kaplan meier groups) of the patient selected in Similar Patients view</li>
<li>Rest of the rows show the kaplan meier groups' values for the selected patient and the similar patients to that particula group in the repository </li>
<li>Clicking on the <b>Statistics</b> button will show a popup providing the information of the repository</li>
</ul>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- Prediction Model Modal -->
<div class="modal fade" id="featureModels" tabindex="-1" role="dialog" aria-labelledby="featureModelsLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title" id="featureModelsLabel">Attributes Used in Predicting The Outcomes</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body" id="featureModelsBody">
<div class="row">
<select class="btn btn-outline btn-grey btn-block dropdown-toggle" style="width: 50%;" id="featureModelSelect">
<!-- <option value="OS">Overall Survival (5 year)</option>
<option value="PRG">Progression (5 Year)</option> -->
</select>
</div>
<div class="row" id="featurePicture"></div>
<!-- <img src="imgs/CoxForest_OS_default.png" style="width: 100%; display: block; margin-left: auto; margin-right: auto;"> -->
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- With Radiomics Modal -->
<div class="modal fade" id="WithRadiomics" tabindex="-1" role="dialog" aria-labelledby="WithRadiomicsLabel" aria-hidden="true">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h3 class="modal-title" id="WithRadiomicsLabel">Radiomic Clusters</h3>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body" id="WithRadiomicsBody">
<!-- <div class="row">
With Radiomics
</div> -->
<div class="row" id="WithRadiomicsPicture"></div>
<img src="imgs/rad_clusters.png" style="width: 100%; display: block; margin-left: auto; margin-right: auto;">
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- Modal -->
<div id="exploreModal" class="modal fade" role="dialog">
<div class="modal-dialog">
<!-- Modal content-->
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal">×</button>
<h4 class="modal-title">Filter Patients</h4>
</div>
<div class="modal-body">
<div class="form-horizontal" id="exploreForm">
<!-- create items programatically -->
</div>
</div>
<div class="modal-footer">
<div class="modal-left-buttons">
<button type="button" class="btn btn-warning" data-dismiss="modal" id="exploreFormReset">
<span class="glyphicon glyphicon-refresh"></span>
Reset Filters
</button>
</div>
<div class="modal-right-buttons">
<button type="button" class="btn btn-success" data-dismiss="modal" id="exploreFormApply">
<span class="glyphicon glyphicon-ok"></span>
Apply
</button>
<button type="button" class="btn btn-danger" data-dismiss="modal" id="exploreFormCancel">
<span class="glyphicon glyphicon-remove"></span>
Cancel
</button>
</div>
</div>
</div>
</div>
</div>
<!-- Modal -->
<div id="addPatientModal" class="modal fade" role="dialog">
<div class="modal-dialog">
<!-- Modal content-->
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal">×</button>
<h4 class="modal-title">Add New Patient</h4>
</div>