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| 1 | <!-- |
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| 2 | ========================================================= |
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| 3 | * Brainchop - v3.0.0 |
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| 4 | ========================================================= |
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| 5 | |||
| 6 | * Discription: A user interface for whole brain segmentation |
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| 7 | * Input shape : [1, D, H, W, 1] e.g. [1, 256, 256, 256, 1] |
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| 8 | * Model : Meshnet or similar lightweigth models |
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| 9 | * |
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| 10 | * Authors: Mohamed Masoud and Sergey Plis - 2023 |
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| 11 | ========================================================= |
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| 12 | |||
| 13 | |||
| 14 | |||
| 15 | ========================================================= |
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| 16 | Brainchop for 3D Brain Segmentation |
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| 17 | ========================================================= |
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| 18 | --> |
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| 19 | <!DOCTYPE html> |
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| 20 | <html> |
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| 21 | <head> |
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| 22 | <meta charset="utf-8"> |
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| 23 | <title>Brainchop </title> |
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| 24 | <link rel="apple-touch-icon" sizes="180x180" href="css/favicon_io/apple-touch-icon.png"> |
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| 25 | <link rel="icon" type="image/png" sizes="32x32" href="css/favicon_io/favicon-32x32.png"> |
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| 26 | <link rel="icon" type="image/png" sizes="16x16" href="css/favicon_io/favicon-16x16.png"> |
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| 27 | <link rel="manifest" href="css/favicon_io/site.webmanifest"> |
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| 28 | |||
| 29 | <link rel="stylesheet" href="css/w3.css"> |
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| 30 | <link rel="stylesheet" href="css/font-awesome-4.7.0/css/font-awesome.min.css"> |
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| 31 | <link rel="stylesheet" type="text/css" href="js/libs/webix/codebase/webix.css"> |
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| 32 | <link rel="stylesheet" type="text/css" href="js/libs/papaya_lib/papaya.css"> |
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| 33 | <link rel="stylesheet" type="text/css" href="css/style.css"> |
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| 34 | <link rel="stylesheet" type="text/css" href="css/brainchop.css"> |
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| 35 | |||
| 36 | |||
| 37 | |||
| 38 | <script src="https://cdn.jsdelivr.net/npm/lodash@4.17.21/lodash.min.js"></script> |
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| 39 | |||
| 40 | |||
| 41 | <script src="https://code.jquery.com/jquery-3.3.1.js" integrity="sha256-2Kok7MbOyxpgUVvAk/HJ2jigOSYS2auK4Pfzbm7uH60=" crossorigin="anonymous"></script> |
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| 42 | <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js" type="text/javascript"></script> |
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| 43 | <script src="https://docs.opencv.org/3.4.0/opencv.js"></script> |
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| 44 | <script src="https://www.lactame.com/lib/image-js/0.21.2/image.min.js"></script> |
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| 45 | |||
| 46 | <script src="js/libs/webix/codebase/webix.js"></script> |
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| 47 | <script src="js/libs/tf.min.js"></script> |
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| 48 | <!-- <script src="https://cdn.jsdelivr.net/npm/@tensorflow/tfjs@3.18.0/dist/tf.min.js"> </script> |
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| 49 | <script src="https://cdn.jsdelivr.net/npm/@tensorflow/tfjs-backend-webgpu/dist/tf-backend-webgpu.js"></script> --> |
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| 50 | <script src="js/libs/float16.js"></script> |
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| 51 | |||
| 52 | <script type="text/javascript" src="js/libs/papaya_lib/papaya.js"></script> |
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| 53 | |||
| 54 | <script type="text/javascript" src="js/libs/nifti-reader.js"></script> |
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| 55 | <script type="text/javascript" src="js/libs/nifti-reader-min.js"></script> |
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| 56 | <script type="text/javascript" src="js/brainchop/connectedComponents3DAll.js"></script> |
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| 57 | |||
| 58 | <script type="module"> |
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| 59 | import { Niivue } from './js/brainchop/Niivue.js'; |
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| 60 | window.Niivue = Niivue; |
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| 61 | </script> |
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| 62 | |||
| 63 | <script type="text/javascript" src="js/brainchop/mainParameters.js"></script> |
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| 64 | <script type="text/javascript" src="js/brainchop/mainMeshNetFunctions.js"></script> |
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| 65 | <script type="text/javascript" src="js/brainchop/mainNiftiReadingFunctions.js"></script> |
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| 66 | <script type="text/javascript" src="js/brainchop/mainTypes.js"></script> |
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| 67 | |||
| 68 | |||
| 69 | <script type="text/javascript" src="js/brainchop/checkCompatibility.js"></script> |
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| 70 | |||
| 71 | <script type="text/javascript" src="js/libs/utilities.js"></script> |
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| 72 | <script type="text/javascript" src="https://cdn.jsdelivr.net/pyodide/v0.20.0/full/pyodide.js"></script> |
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| 73 | <script type="text/javascript" src="js/brainchop/mri_convert.js"></script> |
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| 74 | |||
| 75 | <script type="text/javascript" src="https://cdn.webix.com/components/edge/highcharts/hcharts.js"></script> |
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| 76 | |||
| 77 | <script type="text/javascript" charset="UTF-8" src="js/libs/three/three.js"></script> |
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| 78 | <script type="text/javascript" charset="UTF-8" src="js/libs/three/controls/TrackballControls.js"></script> |
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| 79 | <script type="text/javascript" charset="UTF-8" src="js/libs/three/controls/OrbitControls.js"></script> |
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| 80 | <script type="text/javascript" src="js/libs/util/Stats.js"></script> |
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| 81 | <script type="text/javascript" src="js/libs/util/dat.gui.min.js"></script> |
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| 82 | |||
| 83 | <script type="text/javascript" src="js/libs/util.js"></script> |
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| 84 | <script type="text/javascript" src="js/brainchop/BCBrain3D.js"></script> |
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| 85 | <link rel="stylesheet" href="css/default.css"> |
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| 86 | |||
| 87 | <style> |
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| 88 | /*For Testing*/ |
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| 89 | </style> |
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| 90 | |||
| 91 | |||
| 92 | </head> |
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| 93 | |||
| 94 | <body> |
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| 95 | |||
| 96 | <script type="text/javascript"> |
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| 97 | |||
| 98 | |||
| 99 | webix.ready(function () { |
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| 100 | |||
| 101 | |||
| 102 | // About Window |
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| 103 | let aboutWindowForm = {view: "form", id: "aboutWindowFormId", elements: [ |
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| 104 | |||
| 105 | { cols: [ |
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| 106 | { view: "template", template: "Brainchop is an in-browser automatic segmentation setup for T1 MRI volumes. The tool is an open source and designed to enable users to segment T1 images into regions of interest with a simple interactive interface. The input must be a T1 brain volume in the Nifti format. The output can also be saved as a Nifti file. <br><br> <br><b>Authors:</b> Mohamed Masoud, Farfalla Hu and Sergey Plis (2024).<br> <b>Version:</b> 3.4.0 <br> <b>Funded by:</b> NIH RF1MH121885. <br><br> <b>Special thanks</b> to Kevin Wang and Alex Fedorov for discussions and pre-trained Meshnet models.<br><br> <b>Affiliation: </b> Center for Translational Research in Neuroimaging and Data Science (<a href='https://trendscenter.org/'>TReNDS</a>) <br><center><img src='css/logo/TReNDS_logo.jpg' width='180' height='60'></img></center>" |
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| 107 | |||
| 108 | } |
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| 109 | |||
| 110 | ] |
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| 111 | |||
| 112 | }, |
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| 113 | |||
| 114 | |||
| 115 | { cols: [ |
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| 116 | {}, |
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| 117 | |||
| 118 | { view:"button", value:"Ok", css:"bt_1", width:100, |
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| 119 | align:"center", |
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| 120 | click: function() { |
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| 121 | $$("aboutWindow").hide(); |
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| 122 | } |
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| 123 | }, |
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| 124 | |||
| 125 | {} |
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| 126 | ] |
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| 127 | } |
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| 128 | |||
| 129 | ] |
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| 130 | } |
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| 131 | |||
| 132 | |||
| 133 | |||
| 134 | |||
| 135 | |||
| 136 | // About Window to select local model |
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| 137 | webix.ui({ |
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| 138 | view:"window", |
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| 139 | id: "aboutWindow", |
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| 140 | height:550, |
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| 141 | width:600, |
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| 142 | |||
| 143 | head:{ |
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| 144 | view:"toolbar", css: "toolbarclass", elements:[ |
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| 145 | { type:"header", template:"About", css:"windowtitleclass" }, |
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| 146 | { view:"icon", icon:"wxi-close", click:function(){ |
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| 147 | $$("aboutWindow").hide(); |
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| 148 | } } |
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| 149 | ] |
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| 150 | }, |
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| 151 | |||
| 152 | position:"center", |
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| 153 | body: aboutWindowForm |
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| 154 | |||
| 155 | }) |
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| 156 | |||
| 157 | |||
| 158 | //-- let about = "Demo of 3D MRI Segmentation. <br>By<br> Mohamed Masoud, Sergey Plis (2023) <br> Grant: NIH RF1MH121885 "; |
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| 159 | |||
| 160 | aboutClick = () => { |
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| 161 | $$("aboutWindow").show() |
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| 162 | } |
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| 163 | |||
| 164 | |||
| 165 | |||
| 166 | |||
| 167 | let gl2Temp = document.createElement('canvas').getContext('webgl2') ? |
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| 168 | document.createElement('canvas').getContext('webgl2') : null; |
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| 169 | let maxTextureSize = gl2Temp ? gl2Temp.getParameter(gl2Temp.MAX_TEXTURE_SIZE) : "N/A"; |
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| 170 | |||
| 171 | // Browser Resources Window |
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| 172 | let browserResourcesWindowForm = {view: "form", id: "browserResourcesWindowFormId", elements: [ |
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| 173 | |||
| 174 | { cols: [ |
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| 175 | { view: "template", |
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| 176 | template: " <table>" + |
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| 177 | // "<tr>" + |
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| 178 | // "<th>Model : </th>" + |
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| 179 | // "<td>" + inferenceModelsList[$$("selectModel").getValue() - 1]["modelName"] + "</td>" + |
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| 180 | // "</tr>" + |
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| 181 | |||
| 182 | "<tr>" + |
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| 183 | "<th style='text-align:left'>Browser : </th>" + |
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| 184 | "<td>" + detectBrowser() + "</td>" + |
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| 185 | "</tr>" + |
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| 186 | |||
| 187 | "<tr>" + |
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| 188 | "<th style='text-align:left'>Browser Ver : </th>" + |
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| 189 | "<td>" + detectBrowserVersion() + "</td>" + |
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| 190 | "</tr>" + |
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| 191 | |||
| 192 | "<tr>" + |
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| 193 | "<th style='text-align:left'>Operating Sys. : </th>" + |
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| 194 | "<td>" + detectOperatingSys() + "</td>" + |
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| 195 | "</tr>" + |
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| 196 | |||
| 197 | "<tr>" + |
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| 198 | "<th style='text-align:left'>Texture Size. : </th>" + |
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| 199 | "<td>" + maxTextureSize + "</td>" + |
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| 200 | "</tr>" + |
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| 201 | |||
| 202 | "<tr>" + |
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| 203 | "<th style='text-align:left'>GPU : </th>" + |
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| 204 | "<td>" + detectGPUCardType() + "</td>" + |
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| 205 | "</tr>" + |
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| 206 | |||
| 207 | "<tr>" + |
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| 208 | "<th style='text-align:left'>CPU Cores : </th>" + |
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| 209 | "<td>" + getCPUNumCores()+ "</td>" + |
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| 210 | "</tr>" + |
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| 211 | |||
| 212 | "</table>" + |
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| 213 | "<br><br> - To see a List of tested S/W and H/W with each model please open this <a href='https://docs.google.com/spreadsheets/d/1PU4p6oN4aBfTbXZ8pO6n8fc890Y5Ck0agsIZbm_FO3I/edit#gid=0' target=”_blank”> link. </a> " + |
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| 214 | |||
| 215 | "<br><br> - If the browser above can detect only the internal graphics chip (e.g. HD, UHD), please check the external GPU driver or the system settings to fix the problem and try again." |
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| 216 | |||
| 217 | |||
| 218 | } |
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| 219 | |||
| 220 | ] |
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| 221 | |||
| 222 | }, |
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| 223 | |||
| 224 | |||
| 225 | { cols: [ |
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| 226 | {}, |
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| 227 | |||
| 228 | { view:"button", value:"Ok", css:"bt_1", width:100, |
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| 229 | align:"center", |
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| 230 | click: function() { |
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| 231 | $$("browserResourcesWindow").hide(); |
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| 232 | } |
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| 233 | }, |
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| 234 | |||
| 235 | {} |
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| 236 | ] |
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| 237 | } |
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| 238 | |||
| 239 | ] |
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| 240 | } |
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| 241 | |||
| 242 | |||
| 243 | // Browser Resources Window to select local model |
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| 244 | webix.ui({ |
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| 245 | view:"window", |
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| 246 | id: "browserResourcesWindow", |
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| 247 | height:550, |
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| 248 | width:600, |
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| 249 | |||
| 250 | head:{ |
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| 251 | view:"toolbar", css: "toolbarclass", elements:[ |
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| 252 | { type:"header", template:"Browser Resources", css:"windowtitleclass" }, |
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| 253 | { view:"icon", icon:"wxi-close", click:function(){ |
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| 254 | $$("browserResourcesWindow").hide(); |
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| 255 | } } |
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| 256 | ] |
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| 257 | }, |
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| 258 | |||
| 259 | position:"center", |
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| 260 | body: browserResourcesWindowForm |
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| 261 | |||
| 262 | }) |
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| 263 | |||
| 264 | |||
| 265 | browserResourcesClick = () => { |
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| 266 | $$("browserResourcesWindow").show() |
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| 267 | } |
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| 268 | |||
| 269 | |||
| 270 | |||
| 271 | feedbackClick = () => { |
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| 272 | window.open("https://forms.gle/WzUyVEzgCCY2bHo79"); |
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| 273 | } |
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| 274 | |||
| 275 | githubClick = () => { |
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| 276 | window.open("https://github.com/neuroneural/brainchop"); |
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| 277 | } |
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| 278 | |||
| 279 | |||
| 280 | |||
| 281 | toolbar = { |
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| 282 | view: "toolbar", |
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| 283 | css: "toolbarclass", |
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| 284 | id: "myToolbar", |
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| 285 | rows:[{ cols: |
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| 286 | [ |
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| 287 | { view: "label", label: '<img src="css/svg/Artboard2.svg"/>', css: {"color":"black !important", "font-weight": "bold"}, width: 30 }, |
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| 288 | { view: "label", label: '<p>Brain<span>chop</span></p>', css: {"margin":"0!important"}, inputWidth: 100, align: "left" }, |
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| 289 | { view: "label", label: '<i id="resourcesHwSwId" class="fa fa-cogs"/>', |
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| 290 | css: {"color":"black !important", "font-weight": "bold"}, width: 60, align:"right", click: browserResourcesClick, tooltip:"Browser Resources" }, |
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| 291 | { view: "label", label: '<i id="feedbackId" class="fa fa-pencil-square-o"/>', |
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| 292 | css: {"color":"black !important", "font-weight": "bold"}, width: 60, align:"right", click: feedbackClick, tooltip:"Feedback" }, |
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| 293 | { view: "button", id: "About", value: "About", css:"bt_1", width: 100, align: "right", click: aboutClick }, |
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| 294 | { view: "label", label: '', css: {"color":"black !important", "font-weight": "bold"}, width: 80, align:"right", click: githubClick, tooltip:"GitHub" }, |
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| 295 | ] |
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| 296 | } |
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| 297 | ] |
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| 298 | } |
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| 299 | |||
| 300 | closeMriConvPrgBarWin = () => { |
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| 301 | $$("mriConvPrgBarWin").hide(); |
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| 302 | } |
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| 303 | |||
| 304 | |||
| 305 | // Progress bar for mri_convert.js |
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| 306 | webix.ui({ |
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| 307 | view:"window", |
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| 308 | id: "mriConvPrgBarWin", |
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| 309 | height:50, |
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| 310 | width:500, |
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| 311 | position:"center", |
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| 312 | head:false, |
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| 313 | body:{ |
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| 314 | template:" <div class='w3-container' style='margin-top: 1vh;' id='mriConvertProgBarDiv' > <div class='w3-border' > <div class='w3-green' style='height:2vh;width:0%;' id='mriConvertProgBar'></div> </div> </div> " |
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| 315 | } |
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| 316 | }); |
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| 317 | |||
| 318 | |||
| 319 | |||
| 320 | //--------------Preprocessing Options -------------// |
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| 321 | |||
| 322 | |||
| 323 | clearInputThreejsWin = () => { |
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| 324 | if(inputSceneRendered) { |
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| 325 | clearScene(inputScene); |
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| 326 | input_gui.domElement.style.display = "none"; |
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| 327 | inputSceneRendered = false; |
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| 328 | } |
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| 329 | |||
| 330 | $$("inputThreejsWinId").hide(); |
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| 331 | } |
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| 332 | |||
| 333 | |||
| 334 | showInputPreprocessWindow = () => { |
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| 335 | var defer = $.Deferred(); |
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| 336 | $$("inputThreejsWinId").show(); |
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| 337 | |||
| 338 | if(! inputSceneRendered) { // if false, render |
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| 339 | document.getElementById("inputLoadingIconDiv").style.display = ""; |
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| 340 | } else { |
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| 341 | document.getElementById("inputLoadingIconDiv").style.display = "none"; |
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| 342 | } |
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| 343 | |||
| 344 | setTimeout(function() { |
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| 345 | defer.resolve(); // When this fires, the code in a().then(/..../); is executed. |
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| 346 | }, 100); |
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| 347 | |||
| 348 | return defer; |
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| 349 | } |
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| 350 | |||
| 351 | |||
| 352 | let inputOptions = {view: "form", css: {"border-radius": "20px"}, id: "inputOptionsId", elements: [ |
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| 353 | |||
| 354 | { cols: [ |
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| 355 | { |
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| 356 | view: "label", label: "Input 3D (Enhancement)", |
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| 357 | id: "preprocessId", |
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| 358 | align: "left" |
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| 359 | }, |
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| 360 | |||
| 361 | { |
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| 362 | view: "label", |
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| 363 | id: "inputPrepIcon", |
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| 364 | label: '<i class="fa fa-cube fa-lg" aria-hidden="true" id="preprocessIcon" style="opacity:0.9;filter:alpha(opacity=90);"/>', |
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| 365 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
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| 366 | width: 25, |
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| 367 | height: 25, |
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| 368 | disabled: false, |
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| 369 | click: function() { |
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| 370 | |||
| 371 | showInputPreprocessWindow().then(res => { |
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| 372 | if(! inputSceneRendered) { // if false, will render scene and gui |
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| 373 | |||
| 374 | // Convert niftiImage arrayBuffer to array |
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| 375 | //-- let imageDataFlat1D = new Uint8Array(niftiImage); |
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| 376 | //-- imageDataFlat1D = [...imageDataFlat1D]; |
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| 377 | |||
| 378 | let imageDataFlat1D = arrayBuffer2Array(niftiImage, niftiHeader.datatypeCode ); |
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| 379 | |||
| 380 | // -- tf.tensor(imageDataFlat1D).max().print() |
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| 381 | |||
| 382 | if( ! isNiftiFileVerified(niftiHeader)) { // To render also non-sampled MRI |
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| 383 | imageDataFlat1D = tf.tidy(() => { |
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| 384 | //Round image data |
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| 385 | let imageDataTensor = tf.round(tf.tensor1d(imageDataFlat1D)); |
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| 386 | //Normalize image data |
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| 387 | return tensor2Array( tf.round(tf.mul(normalizeVolumeData(imageDataTensor), tf.scalar(255)) ) ); |
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| 388 | }); |
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| 389 | } |
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| 390 | |||
| 391 | // convert to 3D // <<<<<<<<<<<<<<<<<<<<<<<<<<< 256 256 256 |
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| 392 | let numSlices = niftiHeader.dims[3]; |
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| 393 | let sliceHeight = niftiHeader.dims[2]; |
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| 394 | let sliceWidth = niftiHeader.dims[1]; |
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| 395 | |||
| 396 | let input = tf.tensor(imageDataFlat1D, [numSlices, sliceHeight , sliceWidth]).reverse(1).arraySync(); |
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| 397 | |||
| 398 | let colorLutObj = {}; |
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| 399 | |||
| 400 | // Find voxel values frequency |
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| 401 | let labelsHistogramMap = arrValuesFreq(imageDataFlat1D); |
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| 402 | |||
| 403 | // Convert map to object |
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| 404 | let labelsHistoObj = map2Object(labelsHistogramMap); |
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| 405 | delete labelsHistoObj['0']; |
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| 406 | |||
| 407 | Object.keys(labelsHistoObj).forEach((labelKey, idx) => { |
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| 408 | colorLutObj[labelKey] = "rgb(" + labelKey + "," + labelKey + "," + labelKey + ")"; |
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| 409 | }) |
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| 410 | |||
| 411 | // clearScene(scene) |
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| 412 | |||
| 413 | initInput(input, "inputThreejsWinId", 'input-threejs-container', "input_gui_container", "inputLoadingIconDiv", rawNiftiData, niftiImage, colorLutObj ); |
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| 414 | |||
| 415 | inputSceneRendered = true; |
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| 416 | |||
| 417 | |||
| 418 | } else { // if already rendered |
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| 419 | input_gui.domElement.style.display = ""; |
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| 420 | } |
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| 421 | }) |
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| 422 | |||
| 423 | } |
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| 424 | } |
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| 425 | |||
| 426 | ] |
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| 427 | }, |
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| 428 | |||
| 429 | |||
| 430 | ] |
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| 431 | } |
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| 432 | |||
| 433 | |||
| 434 | |||
| 435 | // Welcome Window |
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| 436 | let inputThreejsWinForm = {view: "form", id: "inputThreejsWinFormId", elements: [ |
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| 437 | |||
| 438 | { cols: [ |
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| 439 | { view: "template", template: " <div id='input-threejs-container'> <div id='input_gui_container'></div> <div id='inputLoadingIconDiv' class ='panel' style='top: 50%; left: 50%; ' > <i id='inputLoadingIcon' style='font-size:1.4vw; color: gray; background-color: rgba(0,0,0,0);' class='w3-xxxlarge w3-spin fa fa-refresh' ></i> </div> </div> <div id='progressLine' class='progress-line'></div>", |
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| 440 | |||
| 441 | } |
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| 442 | |||
| 443 | ] |
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| 444 | |||
| 445 | }, |
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| 446 | |||
| 447 | |||
| 448 | |||
| 449 | { cols: [ |
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| 450 | {}, |
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| 451 | |||
| 452 | { view:"button", id: "inputApplyId", value:"Apply", css:"bt_1", width:100, |
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| 453 | align:"center", |
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| 454 | disabled: true |
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| 455 | }, |
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| 456 | |||
| 457 | { view:"button", value:"Cancel", css:"bt_1", width:100, |
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| 458 | align:"center", |
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| 459 | click: function() { |
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| 460 | $$("inputThreejsWinId").hide(); |
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| 461 | } |
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| 462 | }, |
||
| 463 | |||
| 464 | { view:"button", id: "inputSaveId", value:"Save Copy", css:"bt_1", width:100, |
||
| 465 | align:"center", |
||
| 466 | disabled: true |
||
| 467 | }, |
||
| 468 | |||
| 469 | {} |
||
| 470 | ] |
||
| 471 | } |
||
| 472 | |||
| 473 | ] |
||
| 474 | } |
||
| 475 | |||
| 476 | |||
| 477 | |||
| 478 | webix.ui({ |
||
| 479 | view:"window", |
||
| 480 | id: "inputThreejsWinId", |
||
| 481 | height: Math.round(window.innerHeight * 0.7), |
||
| 482 | width: Math.round(window.innerWidth * 0.7), |
||
| 483 | move: true, |
||
| 484 | resize: true, |
||
| 485 | //width:400, |
||
| 486 | head:{ |
||
| 487 | view:"toolbar", css: "toolbarclass", elements:[ |
||
| 488 | { type:"header", template: "Input Enhancement", css:"windowtitleclass" }, |
||
| 489 | { view:"icon", icon:"wxi-close", click:function(){ |
||
| 490 | $$("inputThreejsWinId").hide(); |
||
| 491 | input_gui.domElement.style.display="none"; |
||
| 492 | } } |
||
| 493 | ] |
||
| 494 | }, |
||
| 495 | position:"center", |
||
| 496 | body: inputThreejsWinForm |
||
| 497 | // body:{ |
||
| 498 | // // create custom list with checkboxes for different ROI. |
||
| 499 | // template:" <div id='input-threejs-container'> <div id='input_gui_container'></div> <div id='inputLoadingIconDiv' class ='panel' style='top: 50%; left: 50%; ' > <i id='inputLoadingIcon' style='font-size:1.4vw; color: gray; background-color: rgba(0,0,0,0);' class='w3-xxxlarge w3-spin fa fa-refresh' ></i> </div> </div> " |
||
| 500 | // } |
||
| 501 | } |
||
| 502 | ) |
||
| 503 | |||
| 504 | //-----------------Output 3D Options------------------// |
||
| 505 | |||
| 506 | clearOutputThreejsWin = () => { |
||
| 507 | if(outputSceneRendered) { |
||
| 508 | clearScene(outputScene); |
||
| 509 | output_gui.domElement.style.display = "none"; |
||
| 510 | document.getElementById('roiList').style.display = "none"; |
||
| 511 | document.getElementById('roiItems').innerHTML = ''; |
||
| 512 | outputSceneRendered = false; |
||
| 513 | } |
||
| 514 | |||
| 515 | $$("outputThreejsWinId").hide(); |
||
| 516 | } |
||
| 517 | |||
| 518 | webix.ui({ |
||
| 519 | view:"window", |
||
| 520 | id: "outputThreejsWinId", |
||
| 521 | height: Math.round(window.innerHeight * 0.7), |
||
| 522 | width: Math.round(window.innerWidth * 0.7), |
||
| 523 | move: true, |
||
| 524 | resize: true, |
||
| 525 | //width:400, |
||
| 526 | head:{ |
||
| 527 | view:"toolbar", css: "toolbarclass", elements:[ |
||
| 528 | { type:"header", template: "3D Segmentation Regions", css:"windowtitleclass" }, |
||
| 529 | { view:"icon", icon:"wxi-close", click:function(){ |
||
| 530 | $$("outputThreejsWinId").hide(); |
||
| 531 | output_gui.domElement.style.display="none"; |
||
| 532 | } } |
||
| 533 | ] |
||
| 534 | }, |
||
| 535 | |||
| 536 | position:"center", |
||
| 537 | |||
| 538 | |||
| 539 | body:{ |
||
| 540 | //-- create custom list with checkboxes for different ROI. |
||
| 541 | template:" <div id='output-threejs-container'> <div id='output_gui_container'></div> <div id='roiList' class='dropdown-check-list'> <span class='anchor'><p style='color:white; font-size:0.6vw; margin-top: 0em; margin-bottom: 0em;'>Select_ROI</p></span> <ul id='roiItems' class='items'></ul> </div> <div id='loadingIconDiv' class ='panel' style='top: 50%; left: 50%; ' > <i id='loadingIcon' style='font-size:1.4vw; color: gray; background-color: rgba(0,0,0,0);' class='w3-xxxlarge w3-spin fa fa-refresh' ></i> </div> </div> " |
||
| 542 | } |
||
| 543 | }) |
||
| 544 | |||
| 545 | |||
| 546 | //-----------------Open Brain T1 MRI ----------------------------------// |
||
| 547 | |||
| 548 | let referenceImage = { view: "form", css: {"border-radius": "20px"}, id: "referenceImage", elements: [ |
||
| 549 | { type:"header", template:"Open Brain T1 MRI", |
||
| 550 | css: "headerclass" |
||
| 551 | }, |
||
| 552 | |||
| 553 | { cols:[ |
||
| 554 | { view: "label", label: "Select NIfTI file", |
||
| 555 | align: "left" |
||
| 556 | }, |
||
| 557 | |||
| 558 | { |
||
| 559 | view: "uploader" , value: "Browse", width: 100, id:"imageUploader", |
||
| 560 | |||
| 561 | css:"bt_1", |
||
| 562 | align: "left", |
||
| 563 | accept: "image/nii, image/nii.gz", |
||
| 564 | autosend: false, |
||
| 565 | multiple: false, |
||
| 566 | on: { |
||
| 567 | onBeforeFileAdd: function(upload) { |
||
| 568 | let file = upload.file; |
||
| 569 | //--file{name: "test.nii", lastModified: 1548792883000, webkitRelativePath: "", size: 503010, type: ""} |
||
| 570 | if(file["name"].search(".nii") > 0) { |
||
| 571 | |||
| 572 | refFileName = file["name"]; |
||
| 573 | |||
| 574 | let reader = new FileReader(); |
||
| 575 | |||
| 576 | var blob = makeSlice(file, 0, file.size); |
||
| 577 | |||
| 578 | reader.onloadend = function(event) { |
||
| 579 | |||
| 580 | if (event.target.readyState === FileReader.DONE) { |
||
| 581 | //--evt.target.result is : ArrayBuffer { byteLength: 763810 } |
||
| 582 | |||
| 583 | // params_mri["files"] = [file]; |
||
| 584 | // Or |
||
| 585 | params_mri["binaryImages"] = [event.target.result]; |
||
| 586 | |||
| 587 | |||
| 588 | |||
| 589 | // Set 0 for MRI viewer |
||
| 590 | papaya.Container.resetViewer(0, params_mri); |
||
| 591 | papaya.Container.atlas = null; |
||
| 592 | // Set 1 for label viewer, need this step to remove startup image |
||
| 593 | // papaya.Container.resetViewer(1); |
||
| 594 | papayaContainers[1].viewer.resetViewer(); |
||
| 595 | papayaContainers[1].viewer.canvas.removeEventListener('mousemove', mouseMoveHandler); |
||
| 596 | papayaContainers[1].viewer.canvas.removeEventListener('mouseout', mouseOutHandler); |
||
| 597 | |||
| 598 | let startTime = performance.now(); |
||
| 599 | // decompress/check uploaded Nifti data |
||
| 600 | rawNiftiData = getNiftiRawData(event.target.result); |
||
| 601 | |||
| 602 | if(rawNiftiData == null) { |
||
| 603 | let loadingErrorTxt = "This file not Nifti or corrupted. Please try again"; |
||
| 604 | |||
| 605 | webix.alert({ |
||
| 606 | type:"alert-error", |
||
| 607 | width:"35%", |
||
| 608 | text: loadingErrorTxt |
||
| 609 | }); |
||
| 610 | |||
| 611 | $$("segmentBtn").disable(); |
||
| 612 | // Disable input 3d preprocess button |
||
| 613 | $$("inputPrepIcon").disable(); |
||
| 614 | document.getElementById("preprocessIcon").style.opacity = 0.3; |
||
| 615 | document.getElementById("preprocessIcon").style.filter = "alpha(opacity=30)"; |
||
| 616 | return 0; |
||
| 617 | } |
||
| 618 | |||
| 619 | // If new MRI loaded, clear last 3D window if rendered before. |
||
| 620 | clearInputThreejsWin(); |
||
| 621 | $$("inputPrepIcon").enable(); |
||
| 622 | document.getElementById("preprocessIcon").style.opacity = 0.9; |
||
| 623 | document.getElementById("preprocessIcon").style.filter = "alpha(opacity=90)"; |
||
| 624 | |||
| 625 | niftiHeader = readNiftiHeader(rawNiftiData); |
||
| 626 | niftiImage = readNiftiImageData(niftiHeader, rawNiftiData); |
||
| 627 | |||
| 628 | statData["Data_Load"] = ((performance.now() - startTime)/1000).toFixed(4); |
||
| 629 | statData["Resampled"] = null; |
||
| 630 | |||
| 631 | statData["File_Type"] = nifti.isNIFTI1(rawNiftiData) ? "NIFTI-1" : nifti.isNIFTI2(rawNiftiData) ? "NIFTI-2" : "NOT-NIFTI"; |
||
| 632 | statData["Img_Size"] = JSON.stringify([niftiHeader.dims[1], niftiHeader.dims[2], niftiHeader.dims[3]]); |
||
| 633 | statData["Num_Bits_Per_Voxel"] = niftiHeader['numBitsPerVoxel'] ; |
||
| 634 | statData["Data_Type_Code"] = niftiHeader['datatypeCode']; |
||
| 635 | statData["Vox_Offset"] = niftiHeader['vox_offset']; |
||
| 636 | statData["Vox_1mm"] = isVoxelSize1mm(niftiHeader); |
||
| 637 | statData["File_Verified"] = isNiftiFileVerified(niftiHeader); |
||
| 638 | //-- Check if Nifti file is already converted and no need to mri_convert.js |
||
| 639 | if( ! isNiftiFileVerified(niftiHeader)) { |
||
| 640 | |||
| 641 | let reasonTxt = "", actionTxt = "", actionCounter = 0; |
||
| 642 | //-- Check Nifti file shape |
||
| 643 | if( (niftiHeader.dims[1]!= 256) || (niftiHeader.dims[2]!= 256) || (niftiHeader.dims[3]!= 256) ) { |
||
| 644 | reasonTxt = " <br> Image shape should be 256x256x256.<br>"; |
||
| 645 | actionTxt = "reshaped"; |
||
| 646 | actionCounter += 1; |
||
| 647 | $$("segmentBtn").disable(); |
||
| 648 | } |
||
| 649 | //-- Check Nifti file data type |
||
| 650 | if ( (niftiHeader['numBitsPerVoxel'] != 8) || (niftiHeader['datatypeCode'] != 2) ) { |
||
| 651 | reasonTxt = reasonTxt + " <br> Data type should be integer in range 0-255.<br>"; |
||
| 652 | if(actionCounter) { actionTxt += "/" } |
||
| 653 | actionTxt += "scaled "; |
||
| 654 | actionCounter += 1; |
||
| 655 | $$("segmentBtn").disable(); |
||
| 656 | } |
||
| 657 | |||
| 658 | //-- Check Nifti file data type |
||
| 659 | if ( ! isVoxelSize1mm(niftiHeader)) { |
||
| 660 | reasonTxt = reasonTxt + " <br> Voxels should be 1x1x1 mm thickness.<br>"; |
||
| 661 | if(actionCounter) { actionTxt += "/" } |
||
| 662 | actionTxt += "resampled "; |
||
| 663 | actionCounter += 1; |
||
| 664 | $$("segmentBtn").disable(); |
||
| 665 | } |
||
| 666 | |||
| 667 | let alertTxt = "MRI needs to be " + actionTxt.bold() + " for proper results. <br>" + reasonTxt.fontcolor("red").bold() + " <br> For more information please refer to <a href='https://github.com/neuroneural/brainchop/wiki/Input-Data' target='_blank'><b>Input Data</b></a> section."; |
||
| 668 | |||
| 669 | |||
| 670 | webix.confirm({ |
||
| 671 | title:"", |
||
| 672 | ok:"Apply", |
||
| 673 | cancel:"Cancel", |
||
| 674 | type: "confirm-error", |
||
| 675 | width: 500, |
||
| 676 | text: alertTxt |
||
| 677 | }) |
||
| 678 | .then(() => { |
||
| 679 | //--- |
||
| 680 | console.log("Starting mri_convert") |
||
| 681 | let blob = new Blob( params_mri["binaryImages"] , {type: "application/octet-binary;charset=utf-8"}); |
||
| 682 | let rawImgurl = window.URL.createObjectURL(blob); |
||
| 683 | |||
| 684 | mri_convert(rawImgurl, rawNiftiData, file["name"]).then(function(res) { |
||
| 685 | rawNiftiData = res; |
||
| 686 | niftiHeader = readNiftiHeader(rawNiftiData); |
||
| 687 | niftiImage = readNiftiImageData(niftiHeader, rawNiftiData); |
||
| 688 | |||
| 689 | params_mri["binaryImages"] = [rawNiftiData]; |
||
| 690 | papaya.Container.resetViewer(0, params_mri); |
||
| 691 | |||
| 692 | // If still not correctly converted |
||
| 693 | if(! isNiftiFileVerified(niftiHeader)) { |
||
| 694 | webix.alert(" File can not be resampled. <br> For more options please refer to <a href='https://github.com/neuroneural/brainchop/wiki/Input-Data' target='_blank'><b>Input Data</b></a> section."); |
||
| 695 | |||
| 696 | statData["Resampled"] = false; |
||
| 697 | submitTiming2GoogleSheet(statData); |
||
| 698 | |||
| 699 | } else { |
||
| 700 | |||
| 701 | statData["Resampled"] = true; |
||
| 702 | } |
||
| 703 | // enable it for all cases |
||
| 704 | $$("segmentBtn").enable(); |
||
| 705 | |||
| 706 | |||
| 707 | }); |
||
| 708 | |||
| 709 | }) |
||
| 710 | .fail(() => { |
||
| 711 | //--- |
||
| 712 | $$("segmentBtn").disable(); |
||
| 713 | statData["Brainchop_Ver"] = "Cancelled" |
||
| 714 | submitTiming2GoogleSheet(statData); |
||
| 715 | }); |
||
| 716 | |||
| 717 | } else { // Not varified file |
||
| 718 | |||
| 719 | |||
| 720 | if(checkGPU()) { |
||
| 721 | $$("segmentBtn").enable(); |
||
| 722 | } |
||
| 723 | } |
||
| 724 | |||
| 725 | numOfOverlays = 0; |
||
| 726 | $$("downloadBtn").disable(); |
||
| 727 | $$("out3DIcon").disable(); |
||
| 728 | $$("outChartIcon").disable(); |
||
| 729 | document.getElementById("out3D-1").style.opacity = 0.3; |
||
| 730 | document.getElementById("outChart-1").style.opacity = 0.3; |
||
| 731 | document.getElementById("out3D-1").style.filter = "alpha(opacity=30)"; |
||
| 732 | document.getElementById("outChart-1").style.filter = "alpha(opacity=30)"; |
||
| 733 | } |
||
| 734 | }; |
||
| 735 | |||
| 736 | reader.readAsArrayBuffer(blob); |
||
| 737 | |||
| 738 | } else { |
||
| 739 | webix.message("Select Nifti file *.nii / *.nii.gz") |
||
| 740 | |||
| 741 | } |
||
| 742 | |||
| 743 | return false; |
||
| 744 | |||
| 745 | } |
||
| 746 | } |
||
| 747 | } |
||
| 748 | ] |
||
| 749 | } |
||
| 750 | ] |
||
| 751 | } |
||
| 752 | |||
| 753 | // function to get masking model from inferenceModelsList |
||
| 754 | getMaskingModels = () => { |
||
| 755 | return ["", "Full Brain GWM (light)", "Full Brain GWM (H Acc & H Crop)"]; |
||
| 756 | } |
||
| 757 | |||
| 758 | let modelBrowsingForm = {view: "form", id: "modelBrowsingFormId", elements: [ |
||
| 759 | { cols: [ |
||
| 760 | { view: "label", label: "Model*", align: "left"}, |
||
| 761 | { view:"icon", id: "modelIconId", icon:"", align: "left"}, |
||
| 762 | { |
||
| 763 | view: "uploader" , value: "Load", width: 100, id:"modelUploader", |
||
| 764 | |||
| 765 | css:"bt_1", |
||
| 766 | align: "left", |
||
| 767 | accept: "application/json", |
||
| 768 | autosend: false, |
||
| 769 | multiple: false, |
||
| 770 | on: { |
||
| 771 | onBeforeFileAdd: function(upload) { |
||
| 772 | let file = upload.file; |
||
| 773 | modelFile = file; |
||
| 774 | console.log("modelFile :", modelFile) |
||
| 775 | //--file{name: "model.json", lastModified: 1548792883000, webkitRelativePath: "", size: 5030, type: ""} |
||
| 776 | if(modelFile["name"].search(".json") > 0) { |
||
| 777 | let reader = new FileReader(); |
||
| 778 | let blob = makeSlice(file, 0, file.size); |
||
| 779 | reader.onloadend = function(event) { |
||
| 780 | |||
| 781 | if (event.target.readyState === FileReader.DONE) { |
||
| 782 | //--evt.target.result is : ArrayBuffer { byteLength: 763810 } |
||
| 783 | $$("modelIconId").config.icon = "wxi-check"; |
||
| 784 | $$("modelIconId").refresh(); |
||
| 785 | } |
||
| 786 | }; |
||
| 787 | |||
| 788 | reader.readAsArrayBuffer(blob); |
||
| 789 | |||
| 790 | } else { |
||
| 791 | webix.message("Select model json file *.json") |
||
| 792 | |||
| 793 | } |
||
| 794 | |||
| 795 | return false; |
||
| 796 | |||
| 797 | } |
||
| 798 | } |
||
| 799 | } |
||
| 800 | |||
| 801 | |||
| 802 | ] |
||
| 803 | }, |
||
| 804 | |||
| 805 | { cols: [ |
||
| 806 | { view: "label", label: "Weights*", align: "left"}, |
||
| 807 | { view:"icon", id: "weightsIconId", icon:"", align: "left"}, |
||
| 808 | { |
||
| 809 | view: "uploader" , value: "Load", width: 100, id:"weightUploader", |
||
| 810 | |||
| 811 | css:"bt_1", |
||
| 812 | align: "left", |
||
| 813 | accept: "application/bin", |
||
| 814 | autosend: false, |
||
| 815 | multiple: false, |
||
| 816 | on: { |
||
| 817 | onBeforeFileAdd: function(upload) { |
||
| 818 | let file = upload.file; |
||
| 819 | weightFile = file; |
||
| 820 | console.log("weightFile :", weightFile) |
||
| 821 | //--file{name: "weights.bin", lastModified: 1548792883000, webkitRelativePath: "", size: 503010, type: ""} |
||
| 822 | if(weightFile["name"].search(".bin") > 0) { |
||
| 823 | let reader = new FileReader(); |
||
| 824 | |||
| 825 | var blob = makeSlice(file, 0, file.size); |
||
| 826 | |||
| 827 | reader.onloadend = function(event) { |
||
| 828 | |||
| 829 | if (event.target.readyState === FileReader.DONE) { |
||
| 830 | //evt.target.result is : ArrayBuffer { byteLength: 763810 } |
||
| 831 | $$("weightsIconId").config.icon = "wxi-check"; |
||
| 832 | $$("weightsIconId").refresh(); |
||
| 833 | } |
||
| 834 | }; |
||
| 835 | |||
| 836 | reader.readAsArrayBuffer(blob); |
||
| 837 | |||
| 838 | } else { |
||
| 839 | webix.message("Select weights binary file *.bin") |
||
| 840 | |||
| 841 | } |
||
| 842 | |||
| 843 | return false; |
||
| 844 | } |
||
| 845 | } |
||
| 846 | } |
||
| 847 | ] |
||
| 848 | }, |
||
| 849 | |||
| 850 | { cols: [ |
||
| 851 | { view: "label", label: "Labels", align: "left"}, |
||
| 852 | { view:"icon", id: "labelsIconId", icon:"", align: "left"}, |
||
| 853 | { |
||
| 854 | view: "uploader" , value: "Load", width: 100, id:"labelUploader", |
||
| 855 | |||
| 856 | css:"bt_1", |
||
| 857 | align: "left", |
||
| 858 | accept: "application/json", |
||
| 859 | autosend: false, |
||
| 860 | multiple: false, |
||
| 861 | on: { |
||
| 862 | onBeforeFileAdd: function(upload) { |
||
| 863 | let file = upload.file; |
||
| 864 | labelFile = file; |
||
| 865 | console.log("labelFile :", labelFile) |
||
| 866 | //--file{name: "weights.bin", lastModified: 1548792883000, webkitRelativePath: "", size: 503010, type: ""} |
||
| 867 | if(labelFile["name"].search(".json") > 0) { |
||
| 868 | let reader = new FileReader(); |
||
| 869 | |||
| 870 | var blob = makeSlice(file, 0, file.size); |
||
| 871 | |||
| 872 | reader.onloadend = function(event) { |
||
| 873 | |||
| 874 | if (event.target.readyState === FileReader.DONE) { |
||
| 875 | //evt.target.result is : ArrayBuffer { byteLength: 763810 } |
||
| 876 | $$("labelsIconId").config.icon = "wxi-check"; |
||
| 877 | $$("labelsIconId").refresh(); |
||
| 878 | } |
||
| 879 | }; |
||
| 880 | |||
| 881 | reader.readAsArrayBuffer(blob); |
||
| 882 | |||
| 883 | } else { |
||
| 884 | webix.message("Select labels json file *.json") |
||
| 885 | |||
| 886 | } |
||
| 887 | |||
| 888 | return false; |
||
| 889 | } |
||
| 890 | } |
||
| 891 | } |
||
| 892 | ] |
||
| 893 | }, |
||
| 894 | |||
| 895 | { cols: [ |
||
| 896 | { view: "label", label: "Colors", align: "left"}, |
||
| 897 | { view:"icon", id: "colorsIconId", icon:"", align: "left"}, |
||
| 898 | { |
||
| 899 | view: "uploader" , value: "Load", width: 100, id:"colorUploader", |
||
| 900 | |||
| 901 | css:"bt_1", |
||
| 902 | align: "left", |
||
| 903 | accept: "application/json", |
||
| 904 | autosend: false, |
||
| 905 | multiple: false, |
||
| 906 | on: { |
||
| 907 | onBeforeFileAdd: function(upload) { |
||
| 908 | let file = upload.file; |
||
| 909 | colorFile = file; |
||
| 910 | console.log("colorFile :", colorFile) |
||
| 911 | //--file{name: "weights.bin", lastModified: 1548792883000, webkitRelativePath: "", size: 503010, type: ""} |
||
| 912 | if(colorFile["name"].search(".json") > 0) { |
||
| 913 | let reader = new FileReader(); |
||
| 914 | |||
| 915 | var blob = makeSlice(file, 0, file.size); |
||
| 916 | |||
| 917 | reader.onloadend = function(event) { |
||
| 918 | |||
| 919 | if (event.target.readyState === FileReader.DONE) { |
||
| 920 | //--evt.target.result is : ArrayBuffer { byteLength: 763810 } |
||
| 921 | $$("colorsIconId").config.icon = "wxi-check"; |
||
| 922 | $$("colorsIconId").refresh(); |
||
| 923 | |||
| 924 | } |
||
| 925 | }; |
||
| 926 | |||
| 927 | reader.readAsArrayBuffer(blob); |
||
| 928 | |||
| 929 | } else { |
||
| 930 | webix.message("Select colors json file *.json") |
||
| 931 | |||
| 932 | } |
||
| 933 | return false; |
||
| 934 | } |
||
| 935 | } |
||
| 936 | } |
||
| 937 | ] |
||
| 938 | }, |
||
| 939 | |||
| 940 | { cols: [ |
||
| 941 | { view: "label", label: "Transpose Input", |
||
| 942 | align: "left" |
||
| 943 | }, |
||
| 944 | |||
| 945 | { view: "select", |
||
| 946 | id: "transposeStatus", |
||
| 947 | value: 1, |
||
| 948 | options: ["true", "false"] |
||
| 949 | }, |
||
| 950 | |||
| 951 | { |
||
| 952 | view: "label", |
||
| 953 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 954 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 955 | width: 25, |
||
| 956 | height: 25, |
||
| 957 | click: function() { |
||
| 958 | let info = "Transpose 3D MRI input data axis for best inference input orientation." |
||
| 959 | $$("modelTooltip").show(); |
||
| 960 | document.getElementById("tooltipDiv").innerHTML = |
||
| 961 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 962 | |||
| 963 | } |
||
| 964 | } |
||
| 965 | |||
| 966 | ] |
||
| 967 | }, |
||
| 968 | |||
| 969 | |||
| 970 | { cols: [ |
||
| 971 | { view: "label", label: "Input Quantile Norm", |
||
| 972 | align: "left" |
||
| 973 | }, |
||
| 974 | |||
| 975 | { view: "select", |
||
| 976 | id: "quantileNormStatus", |
||
| 977 | value: 1, |
||
| 978 | options: ["false", "true"] |
||
| 979 | }, |
||
| 980 | |||
| 981 | { |
||
| 982 | view: "label", |
||
| 983 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 984 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 985 | width: 25, |
||
| 986 | height: 25, |
||
| 987 | click: function() { |
||
| 988 | let info = "Apply Quantile normalization to input MRI, if false then Min-Max normalization will be applied." |
||
| 989 | $$("modelTooltip").show(); |
||
| 990 | document.getElementById("tooltipDiv").innerHTML = |
||
| 991 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 992 | |||
| 993 | } |
||
| 994 | } |
||
| 995 | |||
| 996 | ] |
||
| 997 | }, |
||
| 998 | |||
| 999 | |||
| 1000 | { cols: [ |
||
| 1001 | { view: "label", label: "Auto Threshold Input", |
||
| 1002 | align: "left" |
||
| 1003 | }, |
||
| 1004 | |||
| 1005 | { |
||
| 1006 | view: "select", |
||
| 1007 | id: "autoThresholdStatus", |
||
| 1008 | value: 1, |
||
| 1009 | options: ["0", "0.1", "0.2"] |
||
| 1010 | }, |
||
| 1011 | |||
| 1012 | { |
||
| 1013 | view: "label", |
||
| 1014 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 1015 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1016 | width: 25, |
||
| 1017 | height: 25, |
||
| 1018 | click: function() { |
||
| 1019 | let info = "For speed-up the inference with limited browser memory, auto thresholding the brain from noisy voxels around it before cropping it and feeding the result to the inference model can lower memory use."; |
||
| 1020 | $$("modelTooltip").show(); |
||
| 1021 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1022 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 1023 | } |
||
| 1024 | } |
||
| 1025 | |||
| 1026 | ] |
||
| 1027 | }, |
||
| 1028 | |||
| 1029 | |||
| 1030 | |||
| 1031 | |||
| 1032 | |||
| 1033 | { cols: [ |
||
| 1034 | { view: "label", label: "Crop Input", |
||
| 1035 | align: "left" |
||
| 1036 | }, |
||
| 1037 | |||
| 1038 | { |
||
| 1039 | view: "select", |
||
| 1040 | id: "cropStatus", |
||
| 1041 | value: 1, |
||
| 1042 | options: ["false", "true"], |
||
| 1043 | on: { |
||
| 1044 | onChange: function(newValue, oldValue, config) { |
||
| 1045 | if(newValue == "true") { |
||
| 1046 | $$("cropPadStatus").enable(); |
||
| 1047 | $$("preModelStatus").enable(); |
||
| 1048 | |||
| 1049 | } else { |
||
| 1050 | $$("cropPadStatus").disable(); |
||
| 1051 | $$("cropPadStatus").setValue(0); |
||
| 1052 | $$("preModelStatus").setValue(""); |
||
| 1053 | $$("filterByMaskStatus").setValue("false"); |
||
| 1054 | } |
||
| 1055 | |||
| 1056 | } |
||
| 1057 | } |
||
| 1058 | }, |
||
| 1059 | |||
| 1060 | { |
||
| 1061 | view: "label", |
||
| 1062 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 1063 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1064 | width: 25, |
||
| 1065 | height: 25, |
||
| 1066 | click: function() { |
||
| 1067 | let info = "For speed-up the inference with limited browser memory, cropping brain from background before feeding the result to the inference model can lower memory use."; |
||
| 1068 | $$("modelTooltip").show(); |
||
| 1069 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1070 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 1071 | } |
||
| 1072 | } |
||
| 1073 | |||
| 1074 | ] |
||
| 1075 | }, |
||
| 1076 | |||
| 1077 | { cols: [ |
||
| 1078 | { view: "label", label: "Crop Padding", |
||
| 1079 | align: "left" |
||
| 1080 | }, |
||
| 1081 | |||
| 1082 | { view: "select", |
||
| 1083 | id: "cropPadStatus", |
||
| 1084 | value: 0, |
||
| 1085 | disabled: true, |
||
| 1086 | options: ["0", "1", "2", "3"] |
||
| 1087 | }, |
||
| 1088 | |||
| 1089 | { |
||
| 1090 | view: "label", |
||
| 1091 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 1092 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1093 | width: 25, |
||
| 1094 | height: 25, |
||
| 1095 | click: function() { |
||
| 1096 | let info = "Add Padding to cropped brain 3D image. "; |
||
| 1097 | $$("modelTooltip").show(); |
||
| 1098 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1099 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 1100 | } |
||
| 1101 | } |
||
| 1102 | |||
| 1103 | ] |
||
| 1104 | }, |
||
| 1105 | |||
| 1106 | { cols: [ |
||
| 1107 | { view: "label", label: "Crop by Pre-Model", |
||
| 1108 | align: "left" |
||
| 1109 | }, |
||
| 1110 | |||
| 1111 | { |
||
| 1112 | view: "select", |
||
| 1113 | id: "preModelStatus", |
||
| 1114 | value: 1, |
||
| 1115 | disabled: true, |
||
| 1116 | options: getMaskingModels(), |
||
| 1117 | on: { |
||
| 1118 | onChange: function(newValue, oldValue, config) { |
||
| 1119 | if(newValue !== "") { |
||
| 1120 | $$("filterByMaskStatus").enable(); |
||
| 1121 | $$("preModelPostprocessStatus").enable(); |
||
| 1122 | |||
| 1123 | } else { |
||
| 1124 | $$("filterByMaskStatus").disable(); |
||
| 1125 | $$("filterByMaskStatus").setValue("false"); |
||
| 1126 | $$("preModelPostprocessStatus").disable(); |
||
| 1127 | $$("preModelPostprocessStatus").setValue("false"); |
||
| 1128 | } |
||
| 1129 | |||
| 1130 | } |
||
| 1131 | } |
||
| 1132 | |||
| 1133 | }, |
||
| 1134 | |||
| 1135 | { |
||
| 1136 | view: "label", |
||
| 1137 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 1138 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1139 | width: 25, |
||
| 1140 | height: 25, |
||
| 1141 | click: function() { |
||
| 1142 | let info = "Select a masking model for cropping the brain."; |
||
| 1143 | $$("modelTooltip").show(); |
||
| 1144 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1145 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 1146 | } |
||
| 1147 | } |
||
| 1148 | |||
| 1149 | |||
| 1150 | ] |
||
| 1151 | }, |
||
| 1152 | |||
| 1153 | |||
| 1154 | { cols: [ |
||
| 1155 | { view: "label", label: "Pre-Model Postprocess", |
||
| 1156 | align: "left" |
||
| 1157 | }, |
||
| 1158 | |||
| 1159 | { |
||
| 1160 | view: "select", |
||
| 1161 | id: "preModelPostprocessStatus", |
||
| 1162 | value: 1, |
||
| 1163 | disabled: true, |
||
| 1164 | options: ["false", "true"] |
||
| 1165 | }, |
||
| 1166 | |||
| 1167 | { |
||
| 1168 | view: "label", |
||
| 1169 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 1170 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1171 | width: 25, |
||
| 1172 | height: 25, |
||
| 1173 | click: function() { |
||
| 1174 | let info = "Select if postprocessing is needed after preModel complete brain masking inference"; |
||
| 1175 | $$("modelTooltip").show(); |
||
| 1176 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1177 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 1178 | } |
||
| 1179 | } |
||
| 1180 | |||
| 1181 | |||
| 1182 | ] |
||
| 1183 | }, |
||
| 1184 | |||
| 1185 | { cols: [ |
||
| 1186 | { view: "label", label: "Filter Output by Mask", |
||
| 1187 | align: "left" |
||
| 1188 | }, |
||
| 1189 | |||
| 1190 | { |
||
| 1191 | view: "select", |
||
| 1192 | id: "filterByMaskStatus", |
||
| 1193 | disabled: true, |
||
| 1194 | value: 1, |
||
| 1195 | options: ["false", "true"] |
||
| 1196 | }, |
||
| 1197 | |||
| 1198 | { |
||
| 1199 | view: "label", |
||
| 1200 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 1201 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1202 | width: 25, |
||
| 1203 | height: 25, |
||
| 1204 | click: function() { |
||
| 1205 | let info = "This is a voxel-wise multiplication of resulted output and the mask resulted from the pre-model inference. This option can be used to clean any wrongly segmented regions (e.g. skull areas) but also it can result in removing some properly segmented regions." |
||
| 1206 | $$("modelTooltip").show(); |
||
| 1207 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1208 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 1209 | } |
||
| 1210 | } |
||
| 1211 | |||
| 1212 | ] |
||
| 1213 | }, |
||
| 1214 | |||
| 1215 | { cols: [ |
||
| 1216 | { view: "label", label: "Sequential Convolution", |
||
| 1217 | align: "left" |
||
| 1218 | }, |
||
| 1219 | |||
| 1220 | { |
||
| 1221 | view: "select", |
||
| 1222 | id: "seqConvStatus", |
||
| 1223 | disabled: false, |
||
| 1224 | value: 1, |
||
| 1225 | options: ["false", "true"] |
||
| 1226 | }, |
||
| 1227 | |||
| 1228 | { |
||
| 1229 | view: "label", |
||
| 1230 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 1231 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1232 | width: 25, |
||
| 1233 | height: 25, |
||
| 1234 | click: function() { |
||
| 1235 | let info = "This is enabling sequential convolution layer instead of the model last layer for segmenation. This option can be used to make large and atlas models run on limited resources browser but it takes longer time for inference." |
||
| 1236 | $$("modelTooltip").show(); |
||
| 1237 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1238 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 1239 | } |
||
| 1240 | } |
||
| 1241 | |||
| 1242 | ] |
||
| 1243 | }, |
||
| 1244 | |||
| 1245 | { cols: [ |
||
| 1246 | { view: "label", label: "Model Name*", |
||
| 1247 | align: "left" |
||
| 1248 | }, |
||
| 1249 | { view: "text", |
||
| 1250 | placeholder: "New Model ", |
||
| 1251 | id: "proposedModelName", |
||
| 1252 | disabled: false, |
||
| 1253 | align: "left" |
||
| 1254 | } |
||
| 1255 | ] |
||
| 1256 | }, |
||
| 1257 | { cols: [ |
||
| 1258 | {}, |
||
| 1259 | { view:"button", value:"Confirm", css:"bt_1", width:100, |
||
| 1260 | align:"center", |
||
| 1261 | click: function() { |
||
| 1262 | |||
| 1263 | if(modelFile && weightFile) { |
||
| 1264 | |||
| 1265 | let newId = parseInt(inferenceModelsList.at(-1)["id"]) + 1; |
||
| 1266 | newId = newId.toString(); |
||
| 1267 | |||
| 1268 | // Model list loaded from browsing |
||
| 1269 | browserModelList.push({id: newId, modelFile: modelFile, weightFile: weightFile, colorFile: colorFile, labelFile: labelFile }); |
||
| 1270 | |||
| 1271 | let labelFileUrl = null; |
||
| 1272 | |||
| 1273 | if(browserModelList.at(-1)["labelFile"]) { |
||
| 1274 | labelFileUrl = URL.createObjectURL(browserModelList.at(-1)["labelFile"]); |
||
| 1275 | } |
||
| 1276 | |||
| 1277 | let colorFileUrl = null; |
||
| 1278 | |||
| 1279 | if(browserModelList.at(-1)["colorFile"]) { |
||
| 1280 | colorFileUrl = URL.createObjectURL(browserModelList.at(-1)["colorFile"]); |
||
| 1281 | } |
||
| 1282 | |||
| 1283 | let newModelName = "New Model " + newId; |
||
| 1284 | if($$("proposedModelName").getValue().length && isLetter($$("proposedModelName").getValue()[0])){ |
||
| 1285 | newModelName = $$("proposedModelName").getValue().trim(); |
||
| 1286 | // Check new imported model name possible redundancy |
||
| 1287 | if ( inferenceModelsList.filter(entry => entry.modelName == newModelName).length ) { |
||
| 1288 | webix.message("Please select unique model name"); |
||
| 1289 | return 0; |
||
| 1290 | } |
||
| 1291 | |||
| 1292 | } else if($$("proposedModelName").getValue().length) { |
||
| 1293 | webix.message("Please select valid model name"); |
||
| 1294 | return 0; |
||
| 1295 | } else if(isLetter($$("proposedModelName").getValue()[0])) { |
||
| 1296 | webix.message("Please select model name"); |
||
| 1297 | return 0; |
||
| 1298 | } |
||
| 1299 | |||
| 1300 | let preModelIdVal = null; |
||
| 1301 | if($$("preModelStatus").getValue().length ){ |
||
| 1302 | preModelIdVal = inferenceModelsList.filter(entry => entry.modelName === $$("preModelStatus").getValue())[0].id; |
||
| 1303 | |||
| 1304 | } |
||
| 1305 | |||
| 1306 | |||
| 1307 | inferenceModelsList.push({ |
||
| 1308 | id: newId, |
||
| 1309 | type: "Segmentation", |
||
| 1310 | path: null, |
||
| 1311 | modelName: newModelName, |
||
| 1312 | labelsPath: labelFileUrl, |
||
| 1313 | colorsPath: colorFileUrl, |
||
| 1314 | preModelId: preModelIdVal, |
||
| 1315 | preModelPostProcess: ($$("preModelPostprocessStatus").getValue() === 'true'), |
||
| 1316 | isBatchOverlapEnable: false, |
||
| 1317 | numOverlapBatches: 0, |
||
| 1318 | enableTranspose:($$("transposeStatus").getValue() === 'true'), |
||
| 1319 | enableCrop: ($$("cropStatus").getValue() === 'true'), |
||
| 1320 | cropPadding: parseInt($$("cropPadStatus").getValue()), |
||
| 1321 | autoThreshold: parseInt($$("autoThresholdStatus").getValue()), |
||
| 1322 | enableQuantileNorm: ($$("quantileNormStatus").getValue() === 'true'), |
||
| 1323 | filterOutWithPreMask: ($$("filterByMaskStatus").getValue() === 'true'), |
||
| 1324 | enableSeqConv: ($$("seqConvStatus").getValue() === 'true'), |
||
| 1325 | textureSize: 0, |
||
| 1326 | warning: null, |
||
| 1327 | inferenceDelay: 100, |
||
| 1328 | description: "" |
||
| 1329 | }) |
||
| 1330 | |||
| 1331 | |||
| 1332 | selectModelOptions = getSegmentationFormOptions(inferenceModelsList); |
||
| 1333 | $$("selectModel").config.options = selectModelOptions; |
||
| 1334 | $$("selectModel").config.value = parseInt(newId); |
||
| 1335 | $$("selectModel").refresh(); |
||
| 1336 | |||
| 1337 | $$("modelBrowsingWindow").hide(); |
||
| 1338 | $$("proposedModelName").setValue(""); |
||
| 1339 | |||
| 1340 | |||
| 1341 | } else if(weightFile) { |
||
| 1342 | webix.message("Please select the model json file"); |
||
| 1343 | |||
| 1344 | } else { |
||
| 1345 | webix.message("Please select the model weights file"); |
||
| 1346 | } |
||
| 1347 | } |
||
| 1348 | }, |
||
| 1349 | {} |
||
| 1350 | ] |
||
| 1351 | } |
||
| 1352 | |||
| 1353 | ] |
||
| 1354 | } |
||
| 1355 | |||
| 1356 | |||
| 1357 | |||
| 1358 | // Model Browsing Window to select local model |
||
| 1359 | webix.ui({ |
||
| 1360 | view:"window", |
||
| 1361 | id: "modelBrowsingWindow", |
||
| 1362 | height:770, |
||
| 1363 | width:400, |
||
| 1364 | head:{ |
||
| 1365 | view:"toolbar", css: "toolbarclass", elements:[ |
||
| 1366 | { type:"header", template:"Load tfjs Model", css:"windowtitleclass" }, |
||
| 1367 | { view:"icon", icon:"wxi-close", click:function(){ |
||
| 1368 | $$("modelBrowsingWindow").hide(); |
||
| 1369 | $$("proposedModelName").setValue(""); |
||
| 1370 | } } |
||
| 1371 | ] |
||
| 1372 | }, |
||
| 1373 | |||
| 1374 | position:"center", |
||
| 1375 | body: modelBrowsingForm |
||
| 1376 | }) |
||
| 1377 | |||
| 1378 | // Reset check icon |
||
| 1379 | $$("modelBrowsingWindow").attachEvent("onShow", function(){ |
||
| 1380 | $$("weightsIconId").config.icon = ""; |
||
| 1381 | $$("modelIconId").config.icon = ""; |
||
| 1382 | $$("labelsIconId").config.icon = ""; |
||
| 1383 | $$("colorsIconId").config.icon = ""; |
||
| 1384 | $$("weightsIconId").refresh(); |
||
| 1385 | $$("modelIconId").refresh(); |
||
| 1386 | $$("labelsIconId").refresh(); |
||
| 1387 | $$("colorsIconId").refresh(); |
||
| 1388 | $$("cropStatus").setValue("false"); |
||
| 1389 | $$("seqConvStatus").setValue("false"); |
||
| 1390 | modelFile = null; |
||
| 1391 | weightFile = null; |
||
| 1392 | labelFile = null; |
||
| 1393 | colorFile = null; |
||
| 1394 | }); |
||
| 1395 | |||
| 1396 | |||
| 1397 | getSegmentationFormOptions = (modelsList) => { |
||
| 1398 | let selectedOptions = []; |
||
| 1399 | |||
| 1400 | modelsList.forEach( function(modelEntry) { |
||
| 1401 | selectedOptions.push({id: modelEntry["id"], value: modelEntry["modelName"], path: modelEntry["path"] }); |
||
| 1402 | }) |
||
| 1403 | |||
| 1404 | selectedOptions.push({id: "Browse...", value: "Browse...", path: null }); |
||
| 1405 | |||
| 1406 | return selectedOptions |
||
| 1407 | } |
||
| 1408 | |||
| 1409 | // To load models dynamically from inferenceModelsList |
||
| 1410 | let selectModelOptions = getSegmentationFormOptions(inferenceModelsList); |
||
| 1411 | |||
| 1412 | //-- Count total number of models excluding browsing models |
||
| 1413 | numOfModelsWithoutBrowse = inferenceModelsList.length; |
||
| 1414 | |||
| 1415 | |||
| 1416 | onShowWarningCheck = (checkElem) => { |
||
| 1417 | webix.storage.local.put("noShowWarning", document.getElementById("noShowWarningId").checked); |
||
| 1418 | } |
||
| 1419 | |||
| 1420 | fetchModelWarningStatus = () => { |
||
| 1421 | return webix.storage.local.get("noShowWarning"); |
||
| 1422 | } |
||
| 1423 | |||
| 1424 | onShowTooltipCheck = (checkElem) => { |
||
| 1425 | webix.storage.local.put("noShowTooltip", document.getElementById("noShowTooltipId").checked); |
||
| 1426 | |||
| 1427 | } |
||
| 1428 | |||
| 1429 | fetchModelTooltipStatus = () => { |
||
| 1430 | return webix.storage.local.get("noShowTooltip"); |
||
| 1431 | } |
||
| 1432 | |||
| 1433 | getModelinfo = () => { |
||
| 1434 | let modelDescription = inferenceModelsList[$$("selectModel").getValue() - 1]["description"]; |
||
| 1435 | let info = "No info for this model"; |
||
| 1436 | |||
| 1437 | if(modelDescription) { |
||
| 1438 | info = modelDescription; |
||
| 1439 | } |
||
| 1440 | |||
| 1441 | $$("modelTooltip").show(); |
||
| 1442 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1443 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" |
||
| 1444 | } |
||
| 1445 | |||
| 1446 | resestDependency = () => { |
||
| 1447 | //-- For future use |
||
| 1448 | document.getElementById("out3D-1").style.opacity = 0.3; |
||
| 1449 | document.getElementById("outChart-1").style.opacity = 0.3; |
||
| 1450 | document.getElementById("out3D-1").style.filter = "alpha(opacity=30)"; |
||
| 1451 | document.getElementById("outChart-1").style.filter = "alpha(opacity=30)"; |
||
| 1452 | document.getElementById("progressBarChild").parentElement.style.visibility = "hidden"; |
||
| 1453 | document.getElementById("progressBarChild").style.width = 0; |
||
| 1454 | //-- Reset papaya MRI viewer overlay if exists |
||
| 1455 | resetMriViewerOverlay(1); |
||
| 1456 | //-- Reset Label Viewer |
||
| 1457 | resetLabelViewer(); |
||
| 1458 | clearOutputThreejsWin(); |
||
| 1459 | resetMainParameters(); |
||
| 1460 | } |
||
| 1461 | |||
| 1462 | disableControls = () => { |
||
| 1463 | $$("out3DIcon").disable(); |
||
| 1464 | $$("outChartIcon").disable(); |
||
| 1465 | $$("downloadBtn").disable(); |
||
| 1466 | $$("segmentBtn").disable(); |
||
| 1467 | } |
||
| 1468 | |||
| 1469 | newRunInferencePrepare = () => { |
||
| 1470 | var defer = $.Deferred(); |
||
| 1471 | disableControls(); |
||
| 1472 | resestDependency(); |
||
| 1473 | |||
| 1474 | setTimeout(function() { |
||
| 1475 | defer.resolve(); // When this fires, the code in a().then(/..../); is executed. |
||
| 1476 | }, 100); |
||
| 1477 | |||
| 1478 | return defer; |
||
| 1479 | } |
||
| 1480 | |||
| 1481 | let Segmentation = {view: "form", css: {"border-radius": "20px"}, id: "Segmentation", elements: [ |
||
| 1482 | { type:"header", template:"Segmentation Options", |
||
| 1483 | css: "headerclass" |
||
| 1484 | }, |
||
| 1485 | |||
| 1486 | { cols: [ |
||
| 1487 | |||
| 1488 | { view:"select", |
||
| 1489 | label:"Models", |
||
| 1490 | id: "selectModel", |
||
| 1491 | value:1, |
||
| 1492 | options: selectModelOptions, |
||
| 1493 | on:{ |
||
| 1494 | onChange: function(newValue, oldValue, config) { |
||
| 1495 | const selectedModelEntry = selectModelOptions[this.getValue() - 1]; |
||
| 1496 | |||
| 1497 | if(newValue == "Browse...") { |
||
| 1498 | console.log("Browse selected ..") |
||
| 1499 | $$("modelBrowsingWindow").show(); |
||
| 1500 | |||
| 1501 | } else if (selectedModelEntry["path"]) { |
||
| 1502 | modelObject = {}; |
||
| 1503 | const modelEntry = selectModelOptions[this.getValue() - 1]; |
||
| 1504 | |||
| 1505 | let curModelEntry = inferenceModelsList.filter(entry => entry.id == this.getValue().toString())[0]; |
||
| 1506 | |||
| 1507 | let noShowWarningStatus = fetchModelWarningStatus(); |
||
| 1508 | |||
| 1509 | if(! noShowWarningStatus) { |
||
| 1510 | |||
| 1511 | if (curModelEntry["warning"] != null) { |
||
| 1512 | $$("modelTooltip").show(); |
||
| 1513 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1514 | "<i style='font-size:1.4vw' class='fa fa-exclamation-triangle' ></i> <font style='font-size:0.9vw' >  "+ curModelEntry["warning"] +" </font><br><br><input type='checkbox' id='noShowWarningId' onclick='onShowWarningCheck(this)' name='noShowWarning'><label for='noShowWarning' style='color: black'> Don't show again</label>" |
||
| 1515 | |||
| 1516 | } |
||
| 1517 | } |
||
| 1518 | |||
| 1519 | |||
| 1520 | let noShowTooltipStatus = fetchModelTooltipStatus(); |
||
| 1521 | |||
| 1522 | if(! noShowTooltipStatus) { |
||
| 1523 | |||
| 1524 | if (curModelEntry["textureSize"] != 0) { |
||
| 1525 | //--Compare model needed texture size and browser max texture size |
||
| 1526 | if(curModelEntry["textureSize"] > getMaxTextureSize()) { |
||
| 1527 | $$("modelTooltip").show(); |
||
| 1528 | |||
| 1529 | let warningMessage = "Current browser may not able to run selected model. " + curModelEntry["warning"]; |
||
| 1530 | // $$("modelTooltip").config.body.template = |
||
| 1531 | document.getElementById("tooltipDiv").innerHTML = |
||
| 1532 | "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ warningMessage +" </font><br><br><input type='checkbox' id='noShowTooltipId' name='noShowTooltip' onclick='onShowTooltipCheck(this)'><label for='noShowTooltip'> Don't show </label>" |
||
| 1533 | } |
||
| 1534 | } |
||
| 1535 | } |
||
| 1536 | |||
| 1537 | |||
| 1538 | } else { |
||
| 1539 | let modelEntry = browserModelList.filter(entry => entry.id == this.getValue().toString())[0]; |
||
| 1540 | if(! (modelEntry.modelFile && modelEntry.weightFile)) { |
||
| 1541 | |||
| 1542 | $$("segmentBtn").disable(); |
||
| 1543 | } |
||
| 1544 | |||
| 1545 | } |
||
| 1546 | |||
| 1547 | }, |
||
| 1548 | onAfterRender: function() { |
||
| 1549 | const modelEntry = selectModelOptions[this.getValue() - 1]; |
||
| 1550 | |||
| 1551 | if(! modelEntry["path"]) { |
||
| 1552 | |||
| 1553 | let modelEntry = browserModelList.filter(entry => entry.id == this.getValue().toString())[0]; |
||
| 1554 | if(! (modelEntry.modelFile && modelEntry.weightFile)) { |
||
| 1555 | |||
| 1556 | $$("segmentBtn").disable(); |
||
| 1557 | } |
||
| 1558 | } |
||
| 1559 | |||
| 1560 | } |
||
| 1561 | } |
||
| 1562 | }, |
||
| 1563 | |||
| 1564 | |||
| 1565 | { |
||
| 1566 | view: "label", |
||
| 1567 | label: '<img src="css/svg/info-circle-solid.svg"/>', |
||
| 1568 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1569 | width: 25, |
||
| 1570 | height: 25, |
||
| 1571 | click: function() { |
||
| 1572 | getModelinfo(); |
||
| 1573 | } |
||
| 1574 | } |
||
| 1575 | |||
| 1576 | ] |
||
| 1577 | }, |
||
| 1578 | |||
| 1579 | { cols: [ |
||
| 1580 | { |
||
| 1581 | view: "label", label: "Inference", |
||
| 1582 | id: "segmentBtnLabel", |
||
| 1583 | align: "left" |
||
| 1584 | }, |
||
| 1585 | { |
||
| 1586 | view: "button", label: "Run", |
||
| 1587 | css:"bt_1", |
||
| 1588 | disabled: true, |
||
| 1589 | id: "segmentBtn", |
||
| 1590 | align: "left", |
||
| 1591 | click: function() { |
||
| 1592 | |||
| 1593 | // test for requirement |
||
| 1594 | let maxTextureAvail = getMaxTextureSize(); |
||
| 1595 | let requiredTexture = inferenceModelsList[$$("selectModel").getValue() - 1]["textureSize"]; |
||
| 1596 | |||
| 1597 | |||
| 1598 | |||
| 1599 | if( maxTextureAvail >= requiredTexture ) { |
||
| 1600 | |||
| 1601 | newRunInferencePrepare().then(res => { runInference();}) |
||
| 1602 | } else { |
||
| 1603 | webix.alert("This model needs texture size of minimum " + requiredTexture + ", while current browser supports only " + maxTextureAvail); |
||
| 1604 | } |
||
| 1605 | } |
||
| 1606 | } |
||
| 1607 | ] |
||
| 1608 | }, |
||
| 1609 | { content: "progressBarDiv" , height:50} |
||
| 1610 | // { content: "subProgressBarDiv" , height:50}, |
||
| 1611 | |||
| 1612 | ] |
||
| 1613 | } |
||
| 1614 | |||
| 1615 | |||
| 1616 | |||
| 1617 | |||
| 1618 | //--------------------------------------------// |
||
| 1619 | //---------- Output Rendering ----------------// |
||
| 1620 | //--------------------------------------------// |
||
| 1621 | |||
| 1622 | function convertTo3DArrayAndFlip(allOutputSlices3DCC1DimArray, shape) { |
||
| 1623 | const [num_of_slices, slice_height, slice_width] = shape; |
||
| 1624 | // Create a 3D array (as a flattened 1D typed array for efficiency) |
||
| 1625 | const size = num_of_slices * slice_height * slice_width; |
||
| 1626 | const threeDArray = new allOutputSlices3DCC1DimArray.constructor(size); |
||
| 1627 | |||
| 1628 | for (let slice = 0; slice < num_of_slices; slice++) { |
||
| 1629 | for (let row = 0; row < slice_height; row++) { |
||
| 1630 | // Calculate the starting index for this row in the source and destination arrays |
||
| 1631 | const srcStartIndex = (slice * slice_height * slice_width) + (row * slice_width); |
||
| 1632 | const destStartIndex = (slice * slice_height * slice_width) + ((slice_height - row - 1) * slice_width); |
||
| 1633 | |||
| 1634 | // Copy a slice row into the correct position in the 3D array, flipping it in the process |
||
| 1635 | threeDArray.set( |
||
| 1636 | allOutputSlices3DCC1DimArray.subarray(srcStartIndex, srcStartIndex + slice_width), |
||
| 1637 | destStartIndex |
||
| 1638 | ); |
||
| 1639 | } |
||
| 1640 | } |
||
| 1641 | |||
| 1642 | // Convert the flattened typed array back to a nested regular array structure |
||
| 1643 | const nestedArray = []; |
||
| 1644 | for (let slice = 0; slice < num_of_slices; slice++) { |
||
| 1645 | const twoDArray = []; |
||
| 1646 | for (let row = 0; row < slice_height; row++) { |
||
| 1647 | const start = (slice * slice_height * slice_width) + (row * slice_width); |
||
| 1648 | const end = start + slice_width; |
||
| 1649 | twoDArray.push(Array.from(threeDArray.subarray(start, end))); |
||
| 1650 | } |
||
| 1651 | nestedArray.push(twoDArray); |
||
| 1652 | } |
||
| 1653 | |||
| 1654 | return nestedArray; |
||
| 1655 | } |
||
| 1656 | |||
| 1657 | showThreejsWindow = () => { |
||
| 1658 | var defer = $.Deferred(); |
||
| 1659 | $$("outputThreejsWinId").show(); |
||
| 1660 | |||
| 1661 | if(! outputSceneRendered) { // if false, render |
||
| 1662 | document.getElementById("loadingIconDiv").style.display = ""; |
||
| 1663 | } else { |
||
| 1664 | document.getElementById("loadingIconDiv").style.display = "none"; |
||
| 1665 | } |
||
| 1666 | |||
| 1667 | setTimeout(function() { |
||
| 1668 | defer.resolve(); // When this fires, the code in a().then(/..../); is executed. |
||
| 1669 | }, 100); |
||
| 1670 | |||
| 1671 | return defer; |
||
| 1672 | } |
||
| 1673 | |||
| 1674 | let outputOptions = {view: "form", css: {"border-radius": "20px"}, id: "OutputOptionsId", elements: [ |
||
| 1675 | // { type:"header", template:"Output Options", |
||
| 1676 | // css: "headerclass" |
||
| 1677 | // }, |
||
| 1678 | |||
| 1679 | { cols: [ |
||
| 1680 | { |
||
| 1681 | view: "label", label: "Output Volumes", |
||
| 1682 | id: "outChartLabel", |
||
| 1683 | align: "left" |
||
| 1684 | }, |
||
| 1685 | |||
| 1686 | { |
||
| 1687 | view: "label", |
||
| 1688 | id: "outChartIcon", |
||
| 1689 | label: '<img src="css/svg/outChart-1.svg" id="outChart-1" style="opacity:0.3;filter:alpha(opacity=30);"/>', |
||
| 1690 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1691 | width: 25, |
||
| 1692 | height: 25, |
||
| 1693 | disabled: true, |
||
| 1694 | click: function() { |
||
| 1695 | |||
| 1696 | $$("labelsHistogramWinId").show(); |
||
| 1697 | |||
| 1698 | } |
||
| 1699 | } |
||
| 1700 | |||
| 1701 | ] |
||
| 1702 | }, |
||
| 1703 | |||
| 1704 | { cols: [ |
||
| 1705 | { |
||
| 1706 | view: "label", label: "Output 3D", |
||
| 1707 | id: "out3DLabel", |
||
| 1708 | align: "left" |
||
| 1709 | }, |
||
| 1710 | { |
||
| 1711 | view: "label", |
||
| 1712 | id: "out3DIcon", |
||
| 1713 | label: '<img src="css/svg/out3D-1.svg" id="out3D-1" style="opacity:0.3;filter:alpha(opacity=30);"/>', |
||
| 1714 | css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, |
||
| 1715 | width: 25, |
||
| 1716 | height: 25, |
||
| 1717 | disabled: true, |
||
| 1718 | click: function() { |
||
| 1719 | //-- $$("outputThreejsWinId").show(); |
||
| 1720 | showThreejsWindow().then(res => { |
||
| 1721 | if(! outputSceneRendered) { // if false, will render scene and gui |
||
| 1722 | |||
| 1723 | init(convertTo3DArrayAndFlip(outVolumeStatus['out3DArr'],outVolumeStatus['out3DArrShape']), "outputThreejsWinId",'output-threejs-container', "output_gui_container",outVolumeStatus['colorLutObj'], outVolumeStatus['labelsObj']); |
||
| 1724 | |||
| 1725 | outputSceneRendered = true; |
||
| 1726 | document.getElementById("loadingIconDiv").style.display = "none"; |
||
| 1727 | |||
| 1728 | } else { // if already rendered |
||
| 1729 | output_gui.domElement.style.display = ""; |
||
| 1730 | } |
||
| 1731 | }) |
||
| 1732 | } |
||
| 1733 | } |
||
| 1734 | |||
| 1735 | ] |
||
| 1736 | } |
||
| 1737 | ] |
||
| 1738 | } |
||
| 1739 | |||
| 1740 | |||
| 1741 | |||
| 1742 | |||
| 1743 | |||
| 1744 | |||
| 1745 | // Welcome Window |
||
| 1746 | let welcomeWindowForm = {view: "form", id: "welcomeWindowFormId", elements: [ |
||
| 1747 | |||
| 1748 | { cols: [ |
||
| 1749 | { view: "template", template: " <img src='css/svg/Artboard2.svg' width='20%' align='right'>" + |
||
| 1750 | " <p align='justify'> Welcome to brainchop, a"+ " frontend" +" tool for volumetric segmentation of neuroimaging that works locally on the user side.</p>" + |
||
| 1751 | " <p align='justify'> You're viewing a sample T1 (Left) and its tissue segmentation (Right). Brainchop currenlty supports MRI Nifti file format. </p>" + |
||
| 1752 | "<p align='justify'> To see the tool in action please select a model from the list and run the inference. For more information on brainchop please refer to this <a href='https://github.com/neuroneural/brainchop/wiki/' target='_blank'><b> Wiki </b></a> and this <a href='https://trendscenter.org/in-browser-3d-mri-segmentation-brainchop-org/' target='_blank'><b> Blog</b></a>. For questions or sharing ideas please refere to our <b><a href='https://github.com/neuroneural/brainchop/discussions/' target='_blank'> Discussions </a></b> board. </p>" + |
||
| 1753 | " <center> <video id='advVideo' muted width='400' controls poster='https://github.com/neuroneural/brainchop/releases/download/v3.4.0/BrainchopBanner.png'> <source src='https://github.com/neuroneural/brainchop/releases/download/v1.4.0/brainchopV1_3.mp4' type='video/mp4'>Your browser does not support the video tag</video> </center> <br>" + |
||
| 1754 | "<input type='checkbox' id='noShowWelcomeWindow' name='noShowWelcomeWindow'><label for='noShowWelcomeWindow'><font color='black'> Don't show again </font></label>", |
||
| 1755 | |||
| 1756 | on: { |
||
| 1757 | onAfterRender: function() { |
||
| 1758 | if(fetchWelcomeScreenStatus() == null || fetchWelcomeScreenStatus()) { |
||
| 1759 | // document.getElementById('advVideo').muted = false; |
||
| 1760 | } |
||
| 1761 | |||
| 1762 | } |
||
| 1763 | } |
||
| 1764 | |||
| 1765 | } |
||
| 1766 | |||
| 1767 | ] |
||
| 1768 | |||
| 1769 | }, |
||
| 1770 | |||
| 1771 | |||
| 1772 | { cols: [ |
||
| 1773 | {}, |
||
| 1774 | |||
| 1775 | { view:"button", value:"Ok", css:"bt_1", width:100, |
||
| 1776 | align:"center", |
||
| 1777 | click: function() { |
||
| 1778 | $$("welcomeWindow").hide(); |
||
| 1779 | document.getElementById('advVideo').pause(); |
||
| 1780 | webix.storage.local.put("showWelcomeScreen", ! document.getElementById("noShowWelcomeWindow").checked); |
||
| 1781 | } |
||
| 1782 | }, |
||
| 1783 | |||
| 1784 | {} |
||
| 1785 | ] |
||
| 1786 | } |
||
| 1787 | |||
| 1788 | ] |
||
| 1789 | |||
| 1790 | } |
||
| 1791 | |||
| 1792 | |||
| 1793 | webix.ui({ |
||
| 1794 | view:"popup", |
||
| 1795 | id: "modelTooltip", |
||
| 1796 | // head:"<i style='font-size:1.8vw' class='fa fa-info-circle' ></i>", |
||
| 1797 | body:{ |
||
| 1798 | template:"<div id='tooltipDiv' style = 'text-align:justify'></div>" |
||
| 1799 | }, |
||
| 1800 | position: function(state){ |
||
| 1801 | state.width=state.maxWidth*24/100; |
||
| 1802 | state.height= state.maxHeight*15/100; |
||
| 1803 | state.left=(state.maxWidth-state.width)/1.01; |
||
| 1804 | state.top=(state.maxHeight-state.height)/1.1; |
||
| 1805 | } |
||
| 1806 | |||
| 1807 | }); |
||
| 1808 | |||
| 1809 | |||
| 1810 | // Welcome Window to select local model |
||
| 1811 | webix.ui({ |
||
| 1812 | view:"window", |
||
| 1813 | id: "welcomeWindow", |
||
| 1814 | height:620, |
||
| 1815 | width:600, |
||
| 1816 | head:{ |
||
| 1817 | view:"toolbar", css: "toolbarclass", elements:[ |
||
| 1818 | { type:"header", template:"Welcome", css:"windowtitleclass" }, |
||
| 1819 | { view:"icon", icon:"wxi-close", click:function(){ |
||
| 1820 | $$("welcomeWindow").hide(); |
||
| 1821 | document.getElementById('advVideo').pause(); |
||
| 1822 | } } |
||
| 1823 | ] |
||
| 1824 | }, |
||
| 1825 | |||
| 1826 | position:"center", |
||
| 1827 | body: welcomeWindowForm |
||
| 1828 | }) |
||
| 1829 | |||
| 1830 | |||
| 1831 | fetchWelcomeScreenStatus = () => { |
||
| 1832 | return webix.storage.local.get("showWelcomeScreen"); |
||
| 1833 | } |
||
| 1834 | |||
| 1835 | if(fetchWelcomeScreenStatus() == null || fetchWelcomeScreenStatus()) { |
||
| 1836 | $$("welcomeWindow").show(); |
||
| 1837 | } else { |
||
| 1838 | $$("welcomeWindow").hide(); |
||
| 1839 | } |
||
| 1840 | |||
| 1841 | |||
| 1842 | |||
| 1843 | |||
| 1844 | let downloadNiftiFile = {view: "form", css: {"border-radius": "20px"}, id: "downloadNiftiFileId", elements: [ |
||
| 1845 | { type:"header", template:"Save Labels", |
||
| 1846 | css:"headerclass" |
||
| 1847 | }, |
||
| 1848 | |||
| 1849 | { cols: [ |
||
| 1850 | { view: "label", label: "File Name", |
||
| 1851 | align: "left" |
||
| 1852 | }, |
||
| 1853 | { view: "text", |
||
| 1854 | value: "labels.nii", |
||
| 1855 | id: "fileNameToDL", |
||
| 1856 | disabled: false, |
||
| 1857 | align: "left", |
||
| 1858 | on: { |
||
| 1859 | onChange: function(newValue, oldValue, config) { |
||
| 1860 | if(newValue.length && allOutputSlices3DCC1DimArray.length && isLetter(newValue[0])) { |
||
| 1861 | $$("downloadBtn").enable(); |
||
| 1862 | } else { |
||
| 1863 | $$("downloadBtn").disable(); |
||
| 1864 | } |
||
| 1865 | |||
| 1866 | } |
||
| 1867 | } |
||
| 1868 | } |
||
| 1869 | ] |
||
| 1870 | }, |
||
| 1871 | |||
| 1872 | { cols: [ |
||
| 1873 | { view: "label", label: "Labels", |
||
| 1874 | align: "left" |
||
| 1875 | }, |
||
| 1876 | { view: "button", label: "Save", |
||
| 1877 | id: "downloadBtn", |
||
| 1878 | css: "bt_1", |
||
| 1879 | disabled: true, |
||
| 1880 | align: "left", |
||
| 1881 | click: function() { |
||
| 1882 | |||
| 1883 | if(allOutputSlices3DCC1DimArray.length) { |
||
| 1884 | let downloadFileName = $$("fileNameToDL").getValue(); |
||
| 1885 | |||
| 1886 | if(downloadFileName.search(".nii") < 0) { |
||
| 1887 | // if nii extension doesn't exist, then search will return -1 |
||
| 1888 | downloadFileName = downloadFileName + ".nii"; |
||
| 1889 | } |
||
| 1890 | |||
| 1891 | downloadNifti(allOutputSlices3DCC1DimArray, rawNiftiData, downloadFileName); |
||
| 1892 | |||
| 1893 | } else { |
||
| 1894 | webix.message("No download Data"); |
||
| 1895 | } |
||
| 1896 | } |
||
| 1897 | } |
||
| 1898 | ] |
||
| 1899 | } |
||
| 1900 | ] |
||
| 1901 | } |
||
| 1902 | |||
| 1903 | |||
| 1904 | |||
| 1905 | |||
| 1906 | let memoryView = { |
||
| 1907 | view:"chart", |
||
| 1908 | type:"barH", |
||
| 1909 | id:"memoryMonitor", |
||
| 1910 | width:120, |
||
| 1911 | height:10, |
||
| 1912 | value:"#memoryUse#", |
||
| 1913 | gradient:function(gradient){ |
||
| 1914 | gradient.addColorStop(1.0,"#FF0000"); |
||
| 1915 | gradient.addColorStop(0.5,"#FFFF00"); |
||
| 1916 | gradient.addColorStop(0.0,"#00FF22"); |
||
| 1917 | }, |
||
| 1918 | alpha:0.8, |
||
| 1919 | radius:2, |
||
| 1920 | border:false, |
||
| 1921 | xAxis:{ |
||
| 1922 | start:0, |
||
| 1923 | end:100, |
||
| 1924 | step:10, |
||
| 1925 | template:"" |
||
| 1926 | }, |
||
| 1927 | yAxis:{ |
||
| 1928 | template:"" |
||
| 1929 | } |
||
| 1930 | } |
||
| 1931 | |||
| 1932 | |||
| 1933 | let hardwareStatus = {view: "form", css: {"border-radius": "20px"}, id: "hardwareStatusId", elements: [ |
||
| 1934 | { type:"header", template:"Status", |
||
| 1935 | css: "headerclass" |
||
| 1936 | }, |
||
| 1937 | |||
| 1938 | { cols: [ |
||
| 1939 | { view: "label", label: "WebGL-2", width:70, |
||
| 1940 | align: "left" |
||
| 1941 | }, |
||
| 1942 | { |
||
| 1943 | view: "label", label: "<span id='webGl2Status' style='background-color:none; padding-left:0.5vw;'>  </span>", align: "left" |
||
| 1944 | }, |
||
| 1945 | |||
| 1946 | { view: "label", label: "Memory", width:80, |
||
| 1947 | align: "right" |
||
| 1948 | }, // memoryView |
||
| 1949 | { |
||
| 1950 | view: "label", label: "<span id='memoryStatus' style='background-color:none; padding-left:0.5vw;'>  </span>", align: "right" |
||
| 1951 | } |
||
| 1952 | ] |
||
| 1953 | } |
||
| 1954 | ] |
||
| 1955 | } |
||
| 1956 | |||
| 1957 | |||
| 1958 | //-------------------------chart-------------------------// |
||
| 1959 | //-------------------------chart-------------------------// |
||
| 1960 | //-------------------------chart-------------------------// |
||
| 1961 | |||
| 1962 | |||
| 1963 | roiHChart = { type: "space", rows:[ |
||
| 1964 | |||
| 1965 | { |
||
| 1966 | id: "hchart", view:"highchart", |
||
| 1967 | modules:["series-label", "exporting", "export-data", "accessibility"], |
||
| 1968 | settings:{ |
||
| 1969 | chart: { |
||
| 1970 | type: 'column', |
||
| 1971 | width: 800, |
||
| 1972 | // height: 400, |
||
| 1973 | // marginLeft: 0, |
||
| 1974 | // marginRight: 0, |
||
| 1975 | scrollablePlotArea: { |
||
| 1976 | minWidth: 900, |
||
| 1977 | scrollPositionX: 1 |
||
| 1978 | } |
||
| 1979 | }, |
||
| 1980 | |||
| 1981 | title: { |
||
| 1982 | text: '' |
||
| 1983 | }, |
||
| 1984 | subtitle: { |
||
| 1985 | text: '' |
||
| 1986 | }, |
||
| 1987 | credits: { |
||
| 1988 | enabled: false |
||
| 1989 | }, |
||
| 1990 | plotOptions: { |
||
| 1991 | series: { |
||
| 1992 | borderWidth: 1, |
||
| 1993 | borderColor: 'black', |
||
| 1994 | maxPointWidth: 20 |
||
| 1995 | }, |
||
| 1996 | bar: { |
||
| 1997 | dataLabels: { |
||
| 1998 | enabled: true |
||
| 1999 | } |
||
| 2000 | } |
||
| 2001 | }, |
||
| 2002 | xAxis: { |
||
| 2003 | type: 'category', |
||
| 2004 | |||
| 2005 | categories: null, |
||
| 2006 | labels: { |
||
| 2007 | rotation: -45, |
||
| 2008 | step: 1, |
||
| 2009 | style: { |
||
| 2010 | fontSize: '10px', |
||
| 2011 | fontFamily: 'Verdana, sans-serif' |
||
| 2012 | } |
||
| 2013 | } |
||
| 2014 | }, |
||
| 2015 | |||
| 2016 | yAxis: { |
||
| 2017 | min: 0, |
||
| 2018 | // max: 100, |
||
| 2019 | title: { |
||
| 2020 | text: "Histogram Probability" |
||
| 2021 | // align: 'high' |
||
| 2022 | } |
||
| 2023 | }, |
||
| 2024 | |||
| 2025 | legend: { |
||
| 2026 | enabled: false |
||
| 2027 | }, |
||
| 2028 | |||
| 2029 | series: [{ |
||
| 2030 | name: 'volumes', |
||
| 2031 | data: null, |
||
| 2032 | |||
| 2033 | }] |
||
| 2034 | } |
||
| 2035 | } |
||
| 2036 | ] |
||
| 2037 | }; |
||
| 2038 | |||
| 2039 | |||
| 2040 | // Output labels histogram form |
||
| 2041 | let histogramWindowForm = {view: "form", id: "histogramWindowFormId", |
||
| 2042 | elements: [ |
||
| 2043 | roiHChart, |
||
| 2044 | |||
| 2045 | { cols: [ |
||
| 2046 | {}, |
||
| 2047 | |||
| 2048 | { view:"button", value:"Ok", css:"bt_1", width:100, |
||
| 2049 | align:"center", |
||
| 2050 | click: function() { |
||
| 2051 | $$("labelsHistogramWinId").hide(); |
||
| 2052 | } |
||
| 2053 | }, |
||
| 2054 | { view:"button", value:"Save Data", css:"bt_1", width:100, |
||
| 2055 | align:"center", |
||
| 2056 | click: function() { |
||
| 2057 | |||
| 2058 | let labelsHistoObj = outVolumeStatus['labelsHistoObj']; |
||
| 2059 | let fileName = refFileName == "" ? opts.uiSampleName: refFileName; |
||
| 2060 | downloadJsonObj(labelsHistoObj, fileName +"_Seg" + Object.keys(labelsHistoObj).length + "_volumes.json"); |
||
| 2061 | |||
| 2062 | } |
||
| 2063 | }, |
||
| 2064 | |||
| 2065 | {} |
||
| 2066 | ] |
||
| 2067 | } |
||
| 2068 | |||
| 2069 | ] |
||
| 2070 | } |
||
| 2071 | |||
| 2072 | |||
| 2073 | |||
| 2074 | // Output labels histogram Window |
||
| 2075 | webix.ui({ |
||
| 2076 | view:"window", |
||
| 2077 | id: "labelsHistogramWinId", |
||
| 2078 | height:600, |
||
| 2079 | width:800, |
||
| 2080 | move: true, |
||
| 2081 | resize: true, |
||
| 2082 | head:{ |
||
| 2083 | view:"toolbar", css: "toolbarclass", elements:[ |
||
| 2084 | { type:"header", template:"Output Labels", css:"windowtitleclass" }, |
||
| 2085 | { view:"icon", icon:"wxi-close", click:function() { |
||
| 2086 | $$("labelsHistogramWinId").hide(); |
||
| 2087 | } } |
||
| 2088 | ] |
||
| 2089 | }, |
||
| 2090 | |||
| 2091 | position:"center", |
||
| 2092 | body: histogramWindowForm |
||
| 2093 | |||
| 2094 | }) |
||
| 2095 | |||
| 2096 | |||
| 2097 | |||
| 2098 | |||
| 2099 | |||
| 2100 | //-------------------------------------------------------// |
||
| 2101 | //-------------------------Main--------------------------// |
||
| 2102 | //-------------------------------------------------------// |
||
| 2103 | |||
| 2104 | |||
| 2105 | |||
| 2106 | webix.ui({ |
||
| 2107 | margin:5, |
||
| 2108 | rows:[toolbar, |
||
| 2109 | { |
||
| 2110 | margin:20, |
||
| 2111 | padding: 20, |
||
| 2112 | cols: [ |
||
| 2113 | |||
| 2114 | |||
| 2115 | { |
||
| 2116 | view:"form", |
||
| 2117 | scroll:true, |
||
| 2118 | padding:{ |
||
| 2119 | top:0, bottom:0, left:0, right:15 |
||
| 2120 | }, |
||
| 2121 | css:{"background":"#f3f3f6 !important"}, |
||
| 2122 | borderless: true, |
||
| 2123 | |||
| 2124 | elements:[{ margin:2, width: 250, |
||
| 2125 | rows:[ |
||
| 2126 | referenceImage, |
||
| 2127 | inputOptions, |
||
| 2128 | Segmentation, |
||
| 2129 | outputOptions, |
||
| 2130 | downloadNiftiFile, |
||
| 2131 | hardwareStatus, |
||
| 2132 | {} |
||
| 2133 | ] |
||
| 2134 | }] |
||
| 2135 | }, |
||
| 2136 | |||
| 2137 | |||
| 2138 | { rows: [ |
||
| 2139 | { type:"header", template:"MRI Viewer", |
||
| 2140 | css:"headerclass" |
||
| 2141 | }, |
||
| 2142 | { view: "template", content: "papayaMriDiv", borderless:true}, |
||
| 2143 | |||
| 2144 | ] |
||
| 2145 | |||
| 2146 | }, |
||
| 2147 | {rows: [ |
||
| 2148 | { type:"header", template:"Labels Viewer", |
||
| 2149 | css: "headerclass" |
||
| 2150 | }, |
||
| 2151 | { view: "template", content: "papayaLabelDiv", borderless:true}, |
||
| 2152 | |||
| 2153 | ] |
||
| 2154 | } |
||
| 2155 | ] |
||
| 2156 | }], |
||
| 2157 | |||
| 2158 | }); |
||
| 2159 | |||
| 2160 | |||
| 2161 | //-- To excutes immediately after window loading |
||
| 2162 | //-- 0 for MRI viewer, 1 for Label viewer |
||
| 2163 | papayaContainers[0].preferences.smoothDisplay = 'Yes'; |
||
| 2164 | papayaContainers[1].preferences.smoothDisplay = 'No'; |
||
| 2165 | |||
| 2166 | //-- papaya.Container.restartViewer(0, ["data/t1_c.nii.gz"], true); |
||
| 2167 | papaya.Container.restartViewer(1, ["data/labels.nii.gz"], true); |
||
| 2168 | |||
| 2169 | |||
| 2170 | fetch('data/t1_c.nii.gz') |
||
| 2171 | .then((response) => { |
||
| 2172 | if (response.status >= 200 && response.status <= 299) { |
||
| 2173 | return response.blob(); |
||
| 2174 | } else { |
||
| 2175 | throw Error(response.statusText); |
||
| 2176 | } |
||
| 2177 | }) |
||
| 2178 | .then(blob => { |
||
| 2179 | let initFile = new File([blob], "initLoadFile.nii"); |
||
| 2180 | |||
| 2181 | let reader = new FileReader(); |
||
| 2182 | |||
| 2183 | reader.readAsArrayBuffer(initFile); |
||
| 2184 | |||
| 2185 | reader.onload = evt => { |
||
| 2186 | |||
| 2187 | params_mri["binaryImages"] = [evt.target.result]; |
||
| 2188 | papaya.Container.resetViewer(0, params_mri); |
||
| 2189 | |||
| 2190 | let startTime = performance.now(); |
||
| 2191 | // decompress/check uploaded Nifti data |
||
| 2192 | rawNiftiData = getNiftiRawData(evt.target.result); |
||
| 2193 | niftiHeader = readNiftiHeader(rawNiftiData); |
||
| 2194 | niftiImage = readNiftiImageData(niftiHeader, rawNiftiData); |
||
| 2195 | |||
| 2196 | statData["Data_Load"] = ((performance.now() - startTime)/1000).toFixed(4); |
||
| 2197 | |||
| 2198 | statData["File_Type"] = nifti.isNIFTI1(rawNiftiData) ? "NIFTI-1" : |
||
| 2199 | nifti.isNIFTI2(rawNiftiData) ? "NIFTI-2" : "NOT-NIFTI"; |
||
| 2200 | statData["Img_Size"] = JSON.stringify([niftiHeader.dims[1], niftiHeader.dims[2], niftiHeader.dims[3]]); |
||
| 2201 | statData["Num_Bits_Per_Voxel"] = niftiHeader['numBitsPerVoxel'] ; |
||
| 2202 | statData["Data_Type_Code"] = niftiHeader['datatypeCode']; |
||
| 2203 | statData["Vox_Offset"] = niftiHeader['vox_offset']; |
||
| 2204 | statData["Vox_1mm"] = isVoxelSize1mm(niftiHeader); |
||
| 2205 | statData["File_Verified"] = isNiftiFileVerified(niftiHeader); |
||
| 2206 | |||
| 2207 | |||
| 2208 | // // To sync swap view button |
||
| 2209 | // document.getElementById(PAPAYA_CONTROL_MAIN_SWAP_BUTTON_CSS + papayaContainers[0].containerIndex).addEventListener("click", function(){ |
||
| 2210 | // papayaContainers[1].viewer.rotateViews() |
||
| 2211 | |||
| 2212 | // }) |
||
| 2213 | |||
| 2214 | document.getElementById(PAPAYA_CONTROL_MAIN_SWAP_BUTTON_CSS + papayaContainers[0].containerIndex).disabled = true; |
||
| 2215 | |||
| 2216 | numOfOverlays = 0; |
||
| 2217 | if(checkGPU()) { |
||
| 2218 | $$("segmentBtn").enable(); |
||
| 2219 | } |
||
| 2220 | |||
| 2221 | } |
||
| 2222 | |||
| 2223 | }).catch(function() { |
||
| 2224 | console.log("File not found"); |
||
| 2225 | $$("segmentBtn").disable(); |
||
| 2226 | }); |
||
| 2227 | |||
| 2228 | |||
| 2229 | |||
| 2230 | |||
| 2231 | //--Activate annotation for papaya container 1- default |
||
| 2232 | //-- addMouseMoveHandler(inferenceModelsList[$$("selectModel").getValue() - 1]["labelsPath"], 1); |
||
| 2233 | addMouseMoveHandler("./models/GT/labels.json", 1); |
||
| 2234 | |||
| 2235 | |||
| 2236 | document.getElementById(PAPAYA_CONTROL_MAIN_SWAP_BUTTON_CSS + papayaContainers[1].containerIndex).addEventListener("click", function(){ |
||
| 2237 | papayaContainers[0].viewer.rotateViews() |
||
| 2238 | |||
| 2239 | }) |
||
| 2240 | |||
| 2241 | // Check for possible wrongly report or duplicate models ids |
||
| 2242 | checkInferenceModelList(); |
||
| 2243 | |||
| 2244 | |||
| 2245 | }) |
||
| 2246 | |||
| 2247 | |||
| 2248 | |||
| 2249 | </script> |
||
| 2250 | |||
| 2251 | |||
| 2252 | <div class="grid-container" id ="papayaMriDiv"> |
||
| 2253 | <div class="grid-item" id="divMri"> |
||
| 2254 | <div class="papaya" data-params="params_mri"></div> |
||
| 2255 | </div> |
||
| 2256 | <div class="grid-item"> |
||
| 2257 | <input type="text" id="annotOfContainer_0" disabled></input> |
||
| 2258 | </div> |
||
| 2259 | </div> |
||
| 2260 | |||
| 2261 | <div class="grid-container" id ="papayaLabelDiv"> |
||
| 2262 | <div class="grid-item"> |
||
| 2263 | <div class="papaya" data-params="params_label"></div> |
||
| 2264 | </div> |
||
| 2265 | <div class="grid-item"> |
||
| 2266 | <input type="text" id="annotOfContainer_1" disabled></input> |
||
| 2267 | </div> |
||
| 2268 | </div> |
||
| 2269 | |||
| 2270 | |||
| 2271 | <div class="w3-container" style="margin-top: 0.5vh;" id="progressBarDiv" > |
||
| 2272 | <div class="w3-border" style="visibility: hidden;"> |
||
| 2273 | <div class="w3-blue" style="height:0.75vh;width:0%;" id="progressBarChild"></div> |
||
| 2274 | </div> |
||
| 2275 | <div class="w3-border" style="margin-top: 0.75vh"> |
||
| 2276 | <div class="w3-blue" style="height:1.5vh;width:0%;" id="progressBar"></div> |
||
| 2277 | </div> |
||
| 2278 | </div> |
||
| 2279 | <!-- <div class="w3-container" style="margin-top: 1vh;" id="subProgressBarDiv" > |
||
| 2280 | <div class="w3-border" > |
||
| 2281 | <div class="w3-blue" style="height:2vh;width:0%;" id="subProgressBar"></div> |
||
| 2282 | </div> |
||
| 2283 | </div> --> |
||
| 2284 | |||
| 2285 | |||
| 2286 | <div style="height: 0vh; width: 0vw;" > |
||
| 2287 | <form method="post" autocomplete="off" name="google-sheet" id="googleSubForm" style="visibility: hidden;"> |
||
| 2288 | <input type="text" name="Brainchop_Ver" id= "Brainchop_Ver" /> |
||
| 2289 | <input type="text" name="Country" id= "Country" /> |
||
| 2290 | <input type="text" name="State" id= "State" /> |
||
| 2291 | <input type="text" name="City" id= "City" /> |
||
| 2292 | <input type="text" name="Date" id= "Date" /> |
||
| 2293 | <input type="text" name="Time" id= "Time" /> |
||
| 2294 | <input type="text" name="File_Name" id= "File_Name" /> |
||
| 2295 | <input type="text" name="File_Type" id= "File_Type" /> |
||
| 2296 | <input type="text" name="File_Verified" id= "File_Verified" /> |
||
| 2297 | <input type="text" name="Img_Size" id= "Img_Size" /> |
||
| 2298 | |||
| 2299 | <input type="number" step=any name="Num_Bits_Per_Voxel" id= "Num_Bits_Per_Voxel" /> |
||
| 2300 | <input type="number" step=any name="Data_Type_Code" id= "Data_Type_Code" /> |
||
| 2301 | <input type="number" step=any name="Vox_Offset" id= "Vox_Offset" /> |
||
| 2302 | <input type="text" name="Vox_1mm" id= "Vox_1mm" /> |
||
| 2303 | <input type="text" name="Resampled" id= "Resampled" /> |
||
| 2304 | |||
| 2305 | <input type="text" name="Input_Shape" id= "Input_Shape" /> |
||
| 2306 | <input type="text" name="Output_Shape" id= "Output_Shape" /> |
||
| 2307 | <input type="text" name="Channel_Last" id= "Channel_Last" /> |
||
| 2308 | <input type="number" step=any name="Model_Param" id= "Model_Param" /> |
||
| 2309 | <input type="number" step=any name="Model_Layers" id= "Model_Layers" /> |
||
| 2310 | <input type="number" step=any name="No_SubVolumes" id= "No_SubVolumes" /> |
||
| 2311 | <input type="number" step=any name="Actual_Labels" id= "Actual_Labels" /> |
||
| 2312 | <input type="number" step=any name="Expect_Labels" id= "Expect_Labels" /> |
||
| 2313 | <input type="text" name="NumLabels_Match" id= "NumLabels_Match" /> |
||
| 2314 | <input type="number" step=any name="Data_Load" id= "Data_Load" /> |
||
| 2315 | <input type="number" step=any name="Preprocess_t" id= "Preprocess_t" /> |
||
| 2316 | <input type="number" step=any name="Inference_t" id= "Inference_t" /> |
||
| 2317 | <input type="number" step=any name="Merge_t" id= "Merge_t" /> |
||
| 2318 | <input type="number" step=any name="Postprocess_t" id= "Postprocess_t" /> |
||
| 2319 | <input type="text" name="Model" id= "Model" /> |
||
| 2320 | <input type="text" name="Browser" id= "Browser" /> |
||
| 2321 | <input type="number" step=any name="Browser_Ver" id= "Browser_Ver" /> |
||
| 2322 | <input type="text" name="OS" id= "OS" /> |
||
| 2323 | <input type="number" step=any name="Texture_Size" id= "Texture_Size" /> |
||
| 2324 | <input type="number" step=any name="Heap_Size_MB" id= "Heap_Size_MB" /> |
||
| 2325 | <input type="number" step=any name="Used_Heap_MB" id= "Used_Heap_MB" /> |
||
| 2326 | <input type="number" step=any name="Heap_Limit_MB" id= "Heap_Limit_MB" /> |
||
| 2327 | <input type="text" name="Status" id= "Status" /> |
||
| 2328 | <input type="text" name="WebGL1" id= "WebGL1" /> |
||
| 2329 | <input type="text" name="WebGL2" id= "WebGL2" /> |
||
| 2330 | <input type="text" name="TF_Backend" id= "TF_Backend" /> |
||
| 2331 | <input type="text" name="GPU_Vendor" id= "GPU_Vendor" /> |
||
| 2332 | <input type="text" name="GPU_Card" id= "GPU_Card" /> |
||
| 2333 | <input type="text" name="GPU_Vendor_Full" id= "GPU_Vendor_Full" /> |
||
| 2334 | <input type="text" name="GPU_Card_Full" id= "GPU_Card_Full" /> |
||
| 2335 | <input type="text" name="Error_Type" id= "Error_Type" /> |
||
| 2336 | <input type="text" name="Extra_Err_Info" id= "Extra_Err_Info" /> |
||
| 2337 | <input type="text" name="Extra_Info" id= "Extra_Info" /> |
||
| 2338 | <input type="number" step=any name="CPU_Cores" id= "CPU_Cores" /> |
||
| 2339 | <input type="text" name="Which_Brainchop" id= "Which_Brainchop" /> |
||
| 2340 | <input type="text" name="Seq_Conv" id= "Seq_Conv" /> |
||
| 2341 | <input type="submit" id="SubmitStatisticalData" /> |
||
| 2342 | </form> |
||
| 2343 | </div> |
||
| 2344 | |||
| 2345 | <!-- Credit for github logo: https://github.com/tholman/github-corners --> |
||
| 2346 | <a href="https://github.com/neuroneural/brainchop" style="cursor: pointer;" target='_blank'> |
||
| 2347 | <svg width="80" height="80" viewBox="0 0 250 250" style="position: absolute; top: 0px; right: 0px; border: 0px; cursor: pointer; " aria-hidden="true"> |
||
| 2348 | <path d="M0,0 L115,115 L130,115 L142,142 L250,250 L250,0 Z" fill="#151513" style="cursor: pointer;"></path> |
||
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