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--- a +++ b/v3/index.html @@ -0,0 +1,2355 @@ +<!-- + ========================================================= +* Brainchop - v3.0.0 +========================================================= + +* Discription: A user interface for whole brain segmentation +* Input shape : [1, D, H, W, 1] e.g. [1, 256, 256, 256, 1] +* Model : Meshnet or similar lightweigth models +* +* Authors: Mohamed Masoud and Sergey Plis - 2023 +========================================================= + + + +========================================================= + Brainchop for 3D Brain Segmentation +========================================================= +--> +<!DOCTYPE html> +<html> +<head> + <meta charset="utf-8"> + <title>Brainchop </title> + <link rel="apple-touch-icon" sizes="180x180" href="css/favicon_io/apple-touch-icon.png"> + <link rel="icon" type="image/png" sizes="32x32" href="css/favicon_io/favicon-32x32.png"> + <link rel="icon" type="image/png" sizes="16x16" href="css/favicon_io/favicon-16x16.png"> + <link rel="manifest" href="css/favicon_io/site.webmanifest"> + + <link rel="stylesheet" href="css/w3.css"> + <link rel="stylesheet" href="css/font-awesome-4.7.0/css/font-awesome.min.css"> + <link rel="stylesheet" type="text/css" href="js/libs/webix/codebase/webix.css"> + <link rel="stylesheet" type="text/css" href="js/libs/papaya_lib/papaya.css"> + <link rel="stylesheet" type="text/css" href="css/style.css"> + <link rel="stylesheet" type="text/css" href="css/brainchop.css"> + + + + <script src="https://cdn.jsdelivr.net/npm/lodash@4.17.21/lodash.min.js"></script> + + + <script src="https://code.jquery.com/jquery-3.3.1.js" integrity="sha256-2Kok7MbOyxpgUVvAk/HJ2jigOSYS2auK4Pfzbm7uH60=" crossorigin="anonymous"></script> + <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js" type="text/javascript"></script> + <script src="https://docs.opencv.org/3.4.0/opencv.js"></script> + <script src="https://www.lactame.com/lib/image-js/0.21.2/image.min.js"></script> + + <script src="js/libs/webix/codebase/webix.js"></script> + <script src="js/libs/tf.min.js"></script> + <!-- <script src="https://cdn.jsdelivr.net/npm/@tensorflow/tfjs@3.18.0/dist/tf.min.js"> </script> + <script src="https://cdn.jsdelivr.net/npm/@tensorflow/tfjs-backend-webgpu/dist/tf-backend-webgpu.js"></script> --> + <script src="js/libs/float16.js"></script> + + <script type="text/javascript" src="js/libs/papaya_lib/papaya.js"></script> + + <script type="text/javascript" src="js/libs/nifti-reader.js"></script> + <script type="text/javascript" src="js/libs/nifti-reader-min.js"></script> + <script type="text/javascript" src="js/brainchop/connectedComponents3DAll.js"></script> + + <script type="module"> + import { Niivue } from './js/brainchop/Niivue.js'; + window.Niivue = Niivue; +</script> + + <script type="text/javascript" src="js/brainchop/mainParameters.js"></script> + <script type="text/javascript" src="js/brainchop/mainMeshNetFunctions.js"></script> + <script type="text/javascript" src="js/brainchop/mainNiftiReadingFunctions.js"></script> + <script type="text/javascript" src="js/brainchop/mainTypes.js"></script> + + + <script type="text/javascript" src="js/brainchop/checkCompatibility.js"></script> + + <script type="text/javascript" src="js/libs/utilities.js"></script> + <script type="text/javascript" src="https://cdn.jsdelivr.net/pyodide/v0.20.0/full/pyodide.js"></script> + <script type="text/javascript" src="js/brainchop/mri_convert.js"></script> + + <script type="text/javascript" src="https://cdn.webix.com/components/edge/highcharts/hcharts.js"></script> + + <script type="text/javascript" charset="UTF-8" src="js/libs/three/three.js"></script> + <script type="text/javascript" charset="UTF-8" src="js/libs/three/controls/TrackballControls.js"></script> + <script type="text/javascript" charset="UTF-8" src="js/libs/three/controls/OrbitControls.js"></script> + <script type="text/javascript" src="js/libs/util/Stats.js"></script> + <script type="text/javascript" src="js/libs/util/dat.gui.min.js"></script> + + <script type="text/javascript" src="js/libs/util.js"></script> + <script type="text/javascript" src="js/brainchop/BCBrain3D.js"></script> + <link rel="stylesheet" href="css/default.css"> + + <style> + /*For Testing*/ + </style> + + +</head> + +<body> + + <script type="text/javascript"> + + + webix.ready(function () { + + + // About Window + let aboutWindowForm = {view: "form", id: "aboutWindowFormId", elements: [ + + { cols: [ + { 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>" + + } + + ] + + }, + + + { cols: [ + {}, + + { view:"button", value:"Ok", css:"bt_1", width:100, + align:"center", + click: function() { + $$("aboutWindow").hide(); + } + }, + + {} + ] + } + + ] + } + + + + + + // About Window to select local model + webix.ui({ + view:"window", + id: "aboutWindow", + height:550, + width:600, + + head:{ + view:"toolbar", css: "toolbarclass", elements:[ + { type:"header", template:"About", css:"windowtitleclass" }, + { view:"icon", icon:"wxi-close", click:function(){ + $$("aboutWindow").hide(); + } } + ] + }, + + position:"center", + body: aboutWindowForm + + }) + + + //-- let about = "Demo of 3D MRI Segmentation. <br>By<br> Mohamed Masoud, Sergey Plis (2023) <br> Grant: NIH RF1MH121885 "; + + aboutClick = () => { + $$("aboutWindow").show() + } + + + + + let gl2Temp = document.createElement('canvas').getContext('webgl2') ? + document.createElement('canvas').getContext('webgl2') : null; + let maxTextureSize = gl2Temp ? gl2Temp.getParameter(gl2Temp.MAX_TEXTURE_SIZE) : "N/A"; + + // Browser Resources Window + let browserResourcesWindowForm = {view: "form", id: "browserResourcesWindowFormId", elements: [ + + { cols: [ + { view: "template", + template: " <table>" + + // "<tr>" + + // "<th>Model : </th>" + + // "<td>" + inferenceModelsList[$$("selectModel").getValue() - 1]["modelName"] + "</td>" + + // "</tr>" + + + "<tr>" + + "<th style='text-align:left'>Browser : </th>" + + "<td>" + detectBrowser() + "</td>" + + "</tr>" + + + "<tr>" + + "<th style='text-align:left'>Browser Ver : </th>" + + "<td>" + detectBrowserVersion() + "</td>" + + "</tr>" + + + "<tr>" + + "<th style='text-align:left'>Operating Sys. : </th>" + + "<td>" + detectOperatingSys() + "</td>" + + "</tr>" + + + "<tr>" + + "<th style='text-align:left'>Texture Size. : </th>" + + "<td>" + maxTextureSize + "</td>" + + "</tr>" + + + "<tr>" + + "<th style='text-align:left'>GPU : </th>" + + "<td>" + detectGPUCardType() + "</td>" + + "</tr>" + + + "<tr>" + + "<th style='text-align:left'>CPU Cores : </th>" + + "<td>" + getCPUNumCores()+ "</td>" + + "</tr>" + + + "</table>" + + "<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> " + + + "<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." + + + } + + ] + + }, + + + { cols: [ + {}, + + { view:"button", value:"Ok", css:"bt_1", width:100, + align:"center", + click: function() { + $$("browserResourcesWindow").hide(); + } + }, + + {} + ] + } + + ] + } + + + // Browser Resources Window to select local model + webix.ui({ + view:"window", + id: "browserResourcesWindow", + height:550, + width:600, + + head:{ + view:"toolbar", css: "toolbarclass", elements:[ + { type:"header", template:"Browser Resources", css:"windowtitleclass" }, + { view:"icon", icon:"wxi-close", click:function(){ + $$("browserResourcesWindow").hide(); + } } + ] + }, + + position:"center", + body: browserResourcesWindowForm + + }) + + + browserResourcesClick = () => { + $$("browserResourcesWindow").show() + } + + + + feedbackClick = () => { + window.open("https://forms.gle/WzUyVEzgCCY2bHo79"); + } + + githubClick = () => { + window.open("https://github.com/neuroneural/brainchop"); + } + + + + toolbar = { + view: "toolbar", + css: "toolbarclass", + id: "myToolbar", + rows:[{ cols: + [ + { view: "label", label: '<img src="css/svg/Artboard2.svg"/>', css: {"color":"black !important", "font-weight": "bold"}, width: 30 }, + { view: "label", label: '<p>Brain<span>chop</span></p>', css: {"margin":"0!important"}, inputWidth: 100, align: "left" }, + { view: "label", label: '<i id="resourcesHwSwId" class="fa fa-cogs"/>', + css: {"color":"black !important", "font-weight": "bold"}, width: 60, align:"right", click: browserResourcesClick, tooltip:"Browser Resources" }, + { view: "label", label: '<i id="feedbackId" class="fa fa-pencil-square-o"/>', + css: {"color":"black !important", "font-weight": "bold"}, width: 60, align:"right", click: feedbackClick, tooltip:"Feedback" }, + { view: "button", id: "About", value: "About", css:"bt_1", width: 100, align: "right", click: aboutClick }, + { view: "label", label: '', css: {"color":"black !important", "font-weight": "bold"}, width: 80, align:"right", click: githubClick, tooltip:"GitHub" }, + ] + } + ] + } + + closeMriConvPrgBarWin = () => { + $$("mriConvPrgBarWin").hide(); + } + + + // Progress bar for mri_convert.js + webix.ui({ + view:"window", + id: "mriConvPrgBarWin", + height:50, + width:500, + position:"center", + head:false, + body:{ + 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> " + } + }); + + + + //--------------Preprocessing Options -------------// + + + clearInputThreejsWin = () => { + if(inputSceneRendered) { + clearScene(inputScene); + input_gui.domElement.style.display = "none"; + inputSceneRendered = false; + } + + $$("inputThreejsWinId").hide(); + } + + + showInputPreprocessWindow = () => { + var defer = $.Deferred(); + $$("inputThreejsWinId").show(); + + if(! inputSceneRendered) { // if false, render + document.getElementById("inputLoadingIconDiv").style.display = ""; + } else { + document.getElementById("inputLoadingIconDiv").style.display = "none"; + } + + setTimeout(function() { + defer.resolve(); // When this fires, the code in a().then(/..../); is executed. + }, 100); + + return defer; + } + + + let inputOptions = {view: "form", css: {"border-radius": "20px"}, id: "inputOptionsId", elements: [ + + { cols: [ + { + view: "label", label: "Input 3D (Enhancement)", + id: "preprocessId", + align: "left" + }, + + { + view: "label", + id: "inputPrepIcon", + label: '<i class="fa fa-cube fa-lg" aria-hidden="true" id="preprocessIcon" style="opacity:0.9;filter:alpha(opacity=90);"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + disabled: false, + click: function() { + + showInputPreprocessWindow().then(res => { + if(! inputSceneRendered) { // if false, will render scene and gui + + // Convert niftiImage arrayBuffer to array + //-- let imageDataFlat1D = new Uint8Array(niftiImage); + //-- imageDataFlat1D = [...imageDataFlat1D]; + + let imageDataFlat1D = arrayBuffer2Array(niftiImage, niftiHeader.datatypeCode ); + + // -- tf.tensor(imageDataFlat1D).max().print() + + if( ! isNiftiFileVerified(niftiHeader)) { // To render also non-sampled MRI + imageDataFlat1D = tf.tidy(() => { + //Round image data + let imageDataTensor = tf.round(tf.tensor1d(imageDataFlat1D)); + //Normalize image data + return tensor2Array( tf.round(tf.mul(normalizeVolumeData(imageDataTensor), tf.scalar(255)) ) ); + }); + } + + // convert to 3D // <<<<<<<<<<<<<<<<<<<<<<<<<<< 256 256 256 + let numSlices = niftiHeader.dims[3]; + let sliceHeight = niftiHeader.dims[2]; + let sliceWidth = niftiHeader.dims[1]; + + let input = tf.tensor(imageDataFlat1D, [numSlices, sliceHeight , sliceWidth]).reverse(1).arraySync(); + + let colorLutObj = {}; + + // Find voxel values frequency + let labelsHistogramMap = arrValuesFreq(imageDataFlat1D); + + // Convert map to object + let labelsHistoObj = map2Object(labelsHistogramMap); + delete labelsHistoObj['0']; + + Object.keys(labelsHistoObj).forEach((labelKey, idx) => { + colorLutObj[labelKey] = "rgb(" + labelKey + "," + labelKey + "," + labelKey + ")"; + }) + + // clearScene(scene) + + initInput(input, "inputThreejsWinId", 'input-threejs-container', "input_gui_container", "inputLoadingIconDiv", rawNiftiData, niftiImage, colorLutObj ); + + inputSceneRendered = true; + + + } else { // if already rendered + input_gui.domElement.style.display = ""; + } + }) + + } + } + + ] + }, + + + ] + } + + + + // Welcome Window + let inputThreejsWinForm = {view: "form", id: "inputThreejsWinFormId", elements: [ + + { cols: [ + { 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>", + + } + + ] + + }, + + + + { cols: [ + {}, + + { view:"button", id: "inputApplyId", value:"Apply", css:"bt_1", width:100, + align:"center", + disabled: true + }, + + { view:"button", value:"Cancel", css:"bt_1", width:100, + align:"center", + click: function() { + $$("inputThreejsWinId").hide(); + } + }, + + { view:"button", id: "inputSaveId", value:"Save Copy", css:"bt_1", width:100, + align:"center", + disabled: true + }, + + {} + ] + } + + ] + } + + + + webix.ui({ + view:"window", + id: "inputThreejsWinId", + height: Math.round(window.innerHeight * 0.7), + width: Math.round(window.innerWidth * 0.7), + move: true, + resize: true, + //width:400, + head:{ + view:"toolbar", css: "toolbarclass", elements:[ + { type:"header", template: "Input Enhancement", css:"windowtitleclass" }, + { view:"icon", icon:"wxi-close", click:function(){ + $$("inputThreejsWinId").hide(); + input_gui.domElement.style.display="none"; + } } + ] + }, + position:"center", + body: inputThreejsWinForm + // body:{ + // // create custom list with checkboxes for different ROI. + // 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> " + // } + } + ) + + //-----------------Output 3D Options------------------// + + clearOutputThreejsWin = () => { + if(outputSceneRendered) { + clearScene(outputScene); + output_gui.domElement.style.display = "none"; + document.getElementById('roiList').style.display = "none"; + document.getElementById('roiItems').innerHTML = ''; + outputSceneRendered = false; + } + + $$("outputThreejsWinId").hide(); + } + + webix.ui({ + view:"window", + id: "outputThreejsWinId", + height: Math.round(window.innerHeight * 0.7), + width: Math.round(window.innerWidth * 0.7), + move: true, + resize: true, + //width:400, + head:{ + view:"toolbar", css: "toolbarclass", elements:[ + { type:"header", template: "3D Segmentation Regions", css:"windowtitleclass" }, + { view:"icon", icon:"wxi-close", click:function(){ + $$("outputThreejsWinId").hide(); + output_gui.domElement.style.display="none"; + } } + ] + }, + + position:"center", + + + body:{ + //-- create custom list with checkboxes for different ROI. + 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> " + } + }) + + + //-----------------Open Brain T1 MRI ----------------------------------// + + let referenceImage = { view: "form", css: {"border-radius": "20px"}, id: "referenceImage", elements: [ + { type:"header", template:"Open Brain T1 MRI", + css: "headerclass" + }, + + { cols:[ + { view: "label", label: "Select NIfTI file", + align: "left" + }, + + { + view: "uploader" , value: "Browse", width: 100, id:"imageUploader", + + css:"bt_1", + align: "left", + accept: "image/nii, image/nii.gz", + autosend: false, + multiple: false, + on: { + onBeforeFileAdd: function(upload) { + let file = upload.file; + //--file{name: "test.nii", lastModified: 1548792883000, webkitRelativePath: "", size: 503010, type: ""} + if(file["name"].search(".nii") > 0) { + + refFileName = file["name"]; + + let reader = new FileReader(); + + var blob = makeSlice(file, 0, file.size); + + reader.onloadend = function(event) { + + if (event.target.readyState === FileReader.DONE) { + //--evt.target.result is : ArrayBuffer { byteLength: 763810 } + + // params_mri["files"] = [file]; + // Or + params_mri["binaryImages"] = [event.target.result]; + + + + // Set 0 for MRI viewer + papaya.Container.resetViewer(0, params_mri); + papaya.Container.atlas = null; + // Set 1 for label viewer, need this step to remove startup image + // papaya.Container.resetViewer(1); + papayaContainers[1].viewer.resetViewer(); + papayaContainers[1].viewer.canvas.removeEventListener('mousemove', mouseMoveHandler); + papayaContainers[1].viewer.canvas.removeEventListener('mouseout', mouseOutHandler); + + let startTime = performance.now(); + // decompress/check uploaded Nifti data + rawNiftiData = getNiftiRawData(event.target.result); + + if(rawNiftiData == null) { + let loadingErrorTxt = "This file not Nifti or corrupted. Please try again"; + + webix.alert({ + type:"alert-error", + width:"35%", + text: loadingErrorTxt + }); + + $$("segmentBtn").disable(); + // Disable input 3d preprocess button + $$("inputPrepIcon").disable(); + document.getElementById("preprocessIcon").style.opacity = 0.3; + document.getElementById("preprocessIcon").style.filter = "alpha(opacity=30)"; + return 0; + } + + // If new MRI loaded, clear last 3D window if rendered before. + clearInputThreejsWin(); + $$("inputPrepIcon").enable(); + document.getElementById("preprocessIcon").style.opacity = 0.9; + document.getElementById("preprocessIcon").style.filter = "alpha(opacity=90)"; + + niftiHeader = readNiftiHeader(rawNiftiData); + niftiImage = readNiftiImageData(niftiHeader, rawNiftiData); + + statData["Data_Load"] = ((performance.now() - startTime)/1000).toFixed(4); + statData["Resampled"] = null; + + statData["File_Type"] = nifti.isNIFTI1(rawNiftiData) ? "NIFTI-1" : nifti.isNIFTI2(rawNiftiData) ? "NIFTI-2" : "NOT-NIFTI"; + statData["Img_Size"] = JSON.stringify([niftiHeader.dims[1], niftiHeader.dims[2], niftiHeader.dims[3]]); + statData["Num_Bits_Per_Voxel"] = niftiHeader['numBitsPerVoxel'] ; + statData["Data_Type_Code"] = niftiHeader['datatypeCode']; + statData["Vox_Offset"] = niftiHeader['vox_offset']; + statData["Vox_1mm"] = isVoxelSize1mm(niftiHeader); + statData["File_Verified"] = isNiftiFileVerified(niftiHeader); + //-- Check if Nifti file is already converted and no need to mri_convert.js + if( ! isNiftiFileVerified(niftiHeader)) { + + let reasonTxt = "", actionTxt = "", actionCounter = 0; + //-- Check Nifti file shape + if( (niftiHeader.dims[1]!= 256) || (niftiHeader.dims[2]!= 256) || (niftiHeader.dims[3]!= 256) ) { + reasonTxt = " <br> Image shape should be 256x256x256.<br>"; + actionTxt = "reshaped"; + actionCounter += 1; + $$("segmentBtn").disable(); + } + //-- Check Nifti file data type + if ( (niftiHeader['numBitsPerVoxel'] != 8) || (niftiHeader['datatypeCode'] != 2) ) { + reasonTxt = reasonTxt + " <br> Data type should be integer in range 0-255.<br>"; + if(actionCounter) { actionTxt += "/" } + actionTxt += "scaled "; + actionCounter += 1; + $$("segmentBtn").disable(); + } + + //-- Check Nifti file data type + if ( ! isVoxelSize1mm(niftiHeader)) { + reasonTxt = reasonTxt + " <br> Voxels should be 1x1x1 mm thickness.<br>"; + if(actionCounter) { actionTxt += "/" } + actionTxt += "resampled "; + actionCounter += 1; + $$("segmentBtn").disable(); + } + + 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."; + + + webix.confirm({ + title:"", + ok:"Apply", + cancel:"Cancel", + type: "confirm-error", + width: 500, + text: alertTxt + }) + .then(() => { + //--- + console.log("Starting mri_convert") + let blob = new Blob( params_mri["binaryImages"] , {type: "application/octet-binary;charset=utf-8"}); + let rawImgurl = window.URL.createObjectURL(blob); + + mri_convert(rawImgurl, rawNiftiData, file["name"]).then(function(res) { + rawNiftiData = res; + niftiHeader = readNiftiHeader(rawNiftiData); + niftiImage = readNiftiImageData(niftiHeader, rawNiftiData); + + params_mri["binaryImages"] = [rawNiftiData]; + papaya.Container.resetViewer(0, params_mri); + + // If still not correctly converted + if(! isNiftiFileVerified(niftiHeader)) { + 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."); + + statData["Resampled"] = false; + submitTiming2GoogleSheet(statData); + + } else { + + statData["Resampled"] = true; + } + // enable it for all cases + $$("segmentBtn").enable(); + + + }); + + }) + .fail(() => { + //--- + $$("segmentBtn").disable(); + statData["Brainchop_Ver"] = "Cancelled" + submitTiming2GoogleSheet(statData); + }); + + } else { // Not varified file + + + if(checkGPU()) { + $$("segmentBtn").enable(); + } + } + + numOfOverlays = 0; + $$("downloadBtn").disable(); + $$("out3DIcon").disable(); + $$("outChartIcon").disable(); + document.getElementById("out3D-1").style.opacity = 0.3; + document.getElementById("outChart-1").style.opacity = 0.3; + document.getElementById("out3D-1").style.filter = "alpha(opacity=30)"; + document.getElementById("outChart-1").style.filter = "alpha(opacity=30)"; + } + }; + + reader.readAsArrayBuffer(blob); + + } else { + webix.message("Select Nifti file *.nii / *.nii.gz") + + } + + return false; + + } + } + } + ] + } + ] + } + + // function to get masking model from inferenceModelsList + getMaskingModels = () => { + return ["", "Full Brain GWM (light)", "Full Brain GWM (H Acc & H Crop)"]; + } + + let modelBrowsingForm = {view: "form", id: "modelBrowsingFormId", elements: [ + { cols: [ + { view: "label", label: "Model*", align: "left"}, + { view:"icon", id: "modelIconId", icon:"", align: "left"}, + { + view: "uploader" , value: "Load", width: 100, id:"modelUploader", + + css:"bt_1", + align: "left", + accept: "application/json", + autosend: false, + multiple: false, + on: { + onBeforeFileAdd: function(upload) { + let file = upload.file; + modelFile = file; + console.log("modelFile :", modelFile) + //--file{name: "model.json", lastModified: 1548792883000, webkitRelativePath: "", size: 5030, type: ""} + if(modelFile["name"].search(".json") > 0) { + let reader = new FileReader(); + let blob = makeSlice(file, 0, file.size); + reader.onloadend = function(event) { + + if (event.target.readyState === FileReader.DONE) { + //--evt.target.result is : ArrayBuffer { byteLength: 763810 } + $$("modelIconId").config.icon = "wxi-check"; + $$("modelIconId").refresh(); + } + }; + + reader.readAsArrayBuffer(blob); + + } else { + webix.message("Select model json file *.json") + + } + + return false; + + } + } + } + + + ] + }, + + { cols: [ + { view: "label", label: "Weights*", align: "left"}, + { view:"icon", id: "weightsIconId", icon:"", align: "left"}, + { + view: "uploader" , value: "Load", width: 100, id:"weightUploader", + + css:"bt_1", + align: "left", + accept: "application/bin", + autosend: false, + multiple: false, + on: { + onBeforeFileAdd: function(upload) { + let file = upload.file; + weightFile = file; + console.log("weightFile :", weightFile) + //--file{name: "weights.bin", lastModified: 1548792883000, webkitRelativePath: "", size: 503010, type: ""} + if(weightFile["name"].search(".bin") > 0) { + let reader = new FileReader(); + + var blob = makeSlice(file, 0, file.size); + + reader.onloadend = function(event) { + + if (event.target.readyState === FileReader.DONE) { + //evt.target.result is : ArrayBuffer { byteLength: 763810 } + $$("weightsIconId").config.icon = "wxi-check"; + $$("weightsIconId").refresh(); + } + }; + + reader.readAsArrayBuffer(blob); + + } else { + webix.message("Select weights binary file *.bin") + + } + + return false; + } + } + } + ] + }, + + { cols: [ + { view: "label", label: "Labels", align: "left"}, + { view:"icon", id: "labelsIconId", icon:"", align: "left"}, + { + view: "uploader" , value: "Load", width: 100, id:"labelUploader", + + css:"bt_1", + align: "left", + accept: "application/json", + autosend: false, + multiple: false, + on: { + onBeforeFileAdd: function(upload) { + let file = upload.file; + labelFile = file; + console.log("labelFile :", labelFile) + //--file{name: "weights.bin", lastModified: 1548792883000, webkitRelativePath: "", size: 503010, type: ""} + if(labelFile["name"].search(".json") > 0) { + let reader = new FileReader(); + + var blob = makeSlice(file, 0, file.size); + + reader.onloadend = function(event) { + + if (event.target.readyState === FileReader.DONE) { + //evt.target.result is : ArrayBuffer { byteLength: 763810 } + $$("labelsIconId").config.icon = "wxi-check"; + $$("labelsIconId").refresh(); + } + }; + + reader.readAsArrayBuffer(blob); + + } else { + webix.message("Select labels json file *.json") + + } + + return false; + } + } + } + ] + }, + + { cols: [ + { view: "label", label: "Colors", align: "left"}, + { view:"icon", id: "colorsIconId", icon:"", align: "left"}, + { + view: "uploader" , value: "Load", width: 100, id:"colorUploader", + + css:"bt_1", + align: "left", + accept: "application/json", + autosend: false, + multiple: false, + on: { + onBeforeFileAdd: function(upload) { + let file = upload.file; + colorFile = file; + console.log("colorFile :", colorFile) + //--file{name: "weights.bin", lastModified: 1548792883000, webkitRelativePath: "", size: 503010, type: ""} + if(colorFile["name"].search(".json") > 0) { + let reader = new FileReader(); + + var blob = makeSlice(file, 0, file.size); + + reader.onloadend = function(event) { + + if (event.target.readyState === FileReader.DONE) { + //--evt.target.result is : ArrayBuffer { byteLength: 763810 } + $$("colorsIconId").config.icon = "wxi-check"; + $$("colorsIconId").refresh(); + + } + }; + + reader.readAsArrayBuffer(blob); + + } else { + webix.message("Select colors json file *.json") + + } + return false; + } + } + } + ] + }, + + { cols: [ + { view: "label", label: "Transpose Input", + align: "left" + }, + + { view: "select", + id: "transposeStatus", + value: 1, + options: ["true", "false"] + }, + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + let info = "Transpose 3D MRI input data axis for best inference input orientation." + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + + } + } + + ] + }, + + + { cols: [ + { view: "label", label: "Input Quantile Norm", + align: "left" + }, + + { view: "select", + id: "quantileNormStatus", + value: 1, + options: ["false", "true"] + }, + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + let info = "Apply Quantile normalization to input MRI, if false then Min-Max normalization will be applied." + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + + } + } + + ] + }, + + + { cols: [ + { view: "label", label: "Auto Threshold Input", + align: "left" + }, + + { + view: "select", + id: "autoThresholdStatus", + value: 1, + options: ["0", "0.1", "0.2"] + }, + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + 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."; + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + } + } + + ] + }, + + + + + + { cols: [ + { view: "label", label: "Crop Input", + align: "left" + }, + + { + view: "select", + id: "cropStatus", + value: 1, + options: ["false", "true"], + on: { + onChange: function(newValue, oldValue, config) { + if(newValue == "true") { + $$("cropPadStatus").enable(); + $$("preModelStatus").enable(); + + } else { + $$("cropPadStatus").disable(); + $$("cropPadStatus").setValue(0); + $$("preModelStatus").setValue(""); + $$("filterByMaskStatus").setValue("false"); + } + + } + } + }, + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + let info = "For speed-up the inference with limited browser memory, cropping brain from background before feeding the result to the inference model can lower memory use."; + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + } + } + + ] + }, + + { cols: [ + { view: "label", label: "Crop Padding", + align: "left" + }, + + { view: "select", + id: "cropPadStatus", + value: 0, + disabled: true, + options: ["0", "1", "2", "3"] + }, + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + let info = "Add Padding to cropped brain 3D image. "; + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + } + } + + ] + }, + + { cols: [ + { view: "label", label: "Crop by Pre-Model", + align: "left" + }, + + { + view: "select", + id: "preModelStatus", + value: 1, + disabled: true, + options: getMaskingModels(), + on: { + onChange: function(newValue, oldValue, config) { + if(newValue !== "") { + $$("filterByMaskStatus").enable(); + $$("preModelPostprocessStatus").enable(); + + } else { + $$("filterByMaskStatus").disable(); + $$("filterByMaskStatus").setValue("false"); + $$("preModelPostprocessStatus").disable(); + $$("preModelPostprocessStatus").setValue("false"); + } + + } + } + + }, + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + let info = "Select a masking model for cropping the brain."; + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + } + } + + + ] + }, + + + { cols: [ + { view: "label", label: "Pre-Model Postprocess", + align: "left" + }, + + { + view: "select", + id: "preModelPostprocessStatus", + value: 1, + disabled: true, + options: ["false", "true"] + }, + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + let info = "Select if postprocessing is needed after preModel complete brain masking inference"; + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + } + } + + + ] + }, + + { cols: [ + { view: "label", label: "Filter Output by Mask", + align: "left" + }, + + { + view: "select", + id: "filterByMaskStatus", + disabled: true, + value: 1, + options: ["false", "true"] + }, + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + let info = "This is a voxel-wise multiplication of resulted output and the mask resulted from the pre-model inference. This option can be used to clean any wrongly segmented regions (e.g. skull areas) but also it can result in removing some properly segmented regions." + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + } + } + + ] + }, + + { cols: [ + { view: "label", label: "Sequential Convolution", + align: "left" + }, + + { + view: "select", + id: "seqConvStatus", + disabled: false, + value: 1, + options: ["false", "true"] + }, + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + 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." + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + } + } + + ] + }, + + { cols: [ + { view: "label", label: "Model Name*", + align: "left" + }, + { view: "text", + placeholder: "New Model ", + id: "proposedModelName", + disabled: false, + align: "left" + } + ] + }, + { cols: [ + {}, + { view:"button", value:"Confirm", css:"bt_1", width:100, + align:"center", + click: function() { + + if(modelFile && weightFile) { + + let newId = parseInt(inferenceModelsList.at(-1)["id"]) + 1; + newId = newId.toString(); + + // Model list loaded from browsing + browserModelList.push({id: newId, modelFile: modelFile, weightFile: weightFile, colorFile: colorFile, labelFile: labelFile }); + + let labelFileUrl = null; + + if(browserModelList.at(-1)["labelFile"]) { + labelFileUrl = URL.createObjectURL(browserModelList.at(-1)["labelFile"]); + } + + let colorFileUrl = null; + + if(browserModelList.at(-1)["colorFile"]) { + colorFileUrl = URL.createObjectURL(browserModelList.at(-1)["colorFile"]); + } + + let newModelName = "New Model " + newId; + if($$("proposedModelName").getValue().length && isLetter($$("proposedModelName").getValue()[0])){ + newModelName = $$("proposedModelName").getValue().trim(); + // Check new imported model name possible redundancy + if ( inferenceModelsList.filter(entry => entry.modelName == newModelName).length ) { + webix.message("Please select unique model name"); + return 0; + } + + } else if($$("proposedModelName").getValue().length) { + webix.message("Please select valid model name"); + return 0; + } else if(isLetter($$("proposedModelName").getValue()[0])) { + webix.message("Please select model name"); + return 0; + } + + let preModelIdVal = null; + if($$("preModelStatus").getValue().length ){ + preModelIdVal = inferenceModelsList.filter(entry => entry.modelName === $$("preModelStatus").getValue())[0].id; + + } + + + inferenceModelsList.push({ + id: newId, + type: "Segmentation", + path: null, + modelName: newModelName, + labelsPath: labelFileUrl, + colorsPath: colorFileUrl, + preModelId: preModelIdVal, + preModelPostProcess: ($$("preModelPostprocessStatus").getValue() === 'true'), + isBatchOverlapEnable: false, + numOverlapBatches: 0, + enableTranspose:($$("transposeStatus").getValue() === 'true'), + enableCrop: ($$("cropStatus").getValue() === 'true'), + cropPadding: parseInt($$("cropPadStatus").getValue()), + autoThreshold: parseInt($$("autoThresholdStatus").getValue()), + enableQuantileNorm: ($$("quantileNormStatus").getValue() === 'true'), + filterOutWithPreMask: ($$("filterByMaskStatus").getValue() === 'true'), + enableSeqConv: ($$("seqConvStatus").getValue() === 'true'), + textureSize: 0, + warning: null, + inferenceDelay: 100, + description: "" + }) + + + selectModelOptions = getSegmentationFormOptions(inferenceModelsList); + $$("selectModel").config.options = selectModelOptions; + $$("selectModel").config.value = parseInt(newId); + $$("selectModel").refresh(); + + $$("modelBrowsingWindow").hide(); + $$("proposedModelName").setValue(""); + + + } else if(weightFile) { + webix.message("Please select the model json file"); + + } else { + webix.message("Please select the model weights file"); + } + } + }, + {} + ] + } + + ] + } + + + + // Model Browsing Window to select local model + webix.ui({ + view:"window", + id: "modelBrowsingWindow", + height:770, + width:400, + head:{ + view:"toolbar", css: "toolbarclass", elements:[ + { type:"header", template:"Load tfjs Model", css:"windowtitleclass" }, + { view:"icon", icon:"wxi-close", click:function(){ + $$("modelBrowsingWindow").hide(); + $$("proposedModelName").setValue(""); + } } + ] + }, + + position:"center", + body: modelBrowsingForm + }) + + // Reset check icon + $$("modelBrowsingWindow").attachEvent("onShow", function(){ + $$("weightsIconId").config.icon = ""; + $$("modelIconId").config.icon = ""; + $$("labelsIconId").config.icon = ""; + $$("colorsIconId").config.icon = ""; + $$("weightsIconId").refresh(); + $$("modelIconId").refresh(); + $$("labelsIconId").refresh(); + $$("colorsIconId").refresh(); + $$("cropStatus").setValue("false"); + $$("seqConvStatus").setValue("false"); + modelFile = null; + weightFile = null; + labelFile = null; + colorFile = null; + }); + + + getSegmentationFormOptions = (modelsList) => { + let selectedOptions = []; + + modelsList.forEach( function(modelEntry) { + selectedOptions.push({id: modelEntry["id"], value: modelEntry["modelName"], path: modelEntry["path"] }); + }) + + selectedOptions.push({id: "Browse...", value: "Browse...", path: null }); + + return selectedOptions + } + + // To load models dynamically from inferenceModelsList + let selectModelOptions = getSegmentationFormOptions(inferenceModelsList); + + //-- Count total number of models excluding browsing models + numOfModelsWithoutBrowse = inferenceModelsList.length; + + + onShowWarningCheck = (checkElem) => { + webix.storage.local.put("noShowWarning", document.getElementById("noShowWarningId").checked); + } + + fetchModelWarningStatus = () => { + return webix.storage.local.get("noShowWarning"); + } + + onShowTooltipCheck = (checkElem) => { + webix.storage.local.put("noShowTooltip", document.getElementById("noShowTooltipId").checked); + + } + + fetchModelTooltipStatus = () => { + return webix.storage.local.get("noShowTooltip"); + } + + getModelinfo = () => { + let modelDescription = inferenceModelsList[$$("selectModel").getValue() - 1]["description"]; + let info = "No info for this model"; + + if(modelDescription) { + info = modelDescription; + } + + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<i style='font-size:1.4vw' class='fa fa-info-circle' ></i> <font style='font-size:0.77vw' >  "+ info +" </font>" + } + + resestDependency = () => { + //-- For future use + document.getElementById("out3D-1").style.opacity = 0.3; + document.getElementById("outChart-1").style.opacity = 0.3; + document.getElementById("out3D-1").style.filter = "alpha(opacity=30)"; + document.getElementById("outChart-1").style.filter = "alpha(opacity=30)"; + document.getElementById("progressBarChild").parentElement.style.visibility = "hidden"; + document.getElementById("progressBarChild").style.width = 0; + //-- Reset papaya MRI viewer overlay if exists + resetMriViewerOverlay(1); + //-- Reset Label Viewer + resetLabelViewer(); + clearOutputThreejsWin(); + resetMainParameters(); + } + + disableControls = () => { + $$("out3DIcon").disable(); + $$("outChartIcon").disable(); + $$("downloadBtn").disable(); + $$("segmentBtn").disable(); + } + + newRunInferencePrepare = () => { + var defer = $.Deferred(); + disableControls(); + resestDependency(); + + setTimeout(function() { + defer.resolve(); // When this fires, the code in a().then(/..../); is executed. + }, 100); + + return defer; + } + + let Segmentation = {view: "form", css: {"border-radius": "20px"}, id: "Segmentation", elements: [ + { type:"header", template:"Segmentation Options", + css: "headerclass" + }, + + { cols: [ + + { view:"select", + label:"Models", + id: "selectModel", + value:1, + options: selectModelOptions, + on:{ + onChange: function(newValue, oldValue, config) { + const selectedModelEntry = selectModelOptions[this.getValue() - 1]; + + if(newValue == "Browse...") { + console.log("Browse selected ..") + $$("modelBrowsingWindow").show(); + + } else if (selectedModelEntry["path"]) { + modelObject = {}; + const modelEntry = selectModelOptions[this.getValue() - 1]; + + let curModelEntry = inferenceModelsList.filter(entry => entry.id == this.getValue().toString())[0]; + + let noShowWarningStatus = fetchModelWarningStatus(); + + if(! noShowWarningStatus) { + + if (curModelEntry["warning"] != null) { + $$("modelTooltip").show(); + document.getElementById("tooltipDiv").innerHTML = + "<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>" + + } + } + + + let noShowTooltipStatus = fetchModelTooltipStatus(); + + if(! noShowTooltipStatus) { + + if (curModelEntry["textureSize"] != 0) { + //--Compare model needed texture size and browser max texture size + if(curModelEntry["textureSize"] > getMaxTextureSize()) { + $$("modelTooltip").show(); + + let warningMessage = "Current browser may not able to run selected model. " + curModelEntry["warning"]; + // $$("modelTooltip").config.body.template = + document.getElementById("tooltipDiv").innerHTML = + "<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>" + } + } + } + + + } else { + let modelEntry = browserModelList.filter(entry => entry.id == this.getValue().toString())[0]; + if(! (modelEntry.modelFile && modelEntry.weightFile)) { + + $$("segmentBtn").disable(); + } + + } + + }, + onAfterRender: function() { + const modelEntry = selectModelOptions[this.getValue() - 1]; + + if(! modelEntry["path"]) { + + let modelEntry = browserModelList.filter(entry => entry.id == this.getValue().toString())[0]; + if(! (modelEntry.modelFile && modelEntry.weightFile)) { + + $$("segmentBtn").disable(); + } + } + + } + } + }, + + + { + view: "label", + label: '<img src="css/svg/info-circle-solid.svg"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + click: function() { + getModelinfo(); + } + } + + ] + }, + + { cols: [ + { + view: "label", label: "Inference", + id: "segmentBtnLabel", + align: "left" + }, + { + view: "button", label: "Run", + css:"bt_1", + disabled: true, + id: "segmentBtn", + align: "left", + click: function() { + + // test for requirement + let maxTextureAvail = getMaxTextureSize(); + let requiredTexture = inferenceModelsList[$$("selectModel").getValue() - 1]["textureSize"]; + + + + if( maxTextureAvail >= requiredTexture ) { + + newRunInferencePrepare().then(res => { runInference();}) + } else { + webix.alert("This model needs texture size of minimum " + requiredTexture + ", while current browser supports only " + maxTextureAvail); + } + } + } + ] + }, + { content: "progressBarDiv" , height:50} + // { content: "subProgressBarDiv" , height:50}, + + ] + } + + + + + //--------------------------------------------// + //---------- Output Rendering ----------------// + //--------------------------------------------// + + function convertTo3DArrayAndFlip(allOutputSlices3DCC1DimArray, shape) { + const [num_of_slices, slice_height, slice_width] = shape; + // Create a 3D array (as a flattened 1D typed array for efficiency) + const size = num_of_slices * slice_height * slice_width; + const threeDArray = new allOutputSlices3DCC1DimArray.constructor(size); + + for (let slice = 0; slice < num_of_slices; slice++) { + for (let row = 0; row < slice_height; row++) { + // Calculate the starting index for this row in the source and destination arrays + const srcStartIndex = (slice * slice_height * slice_width) + (row * slice_width); + const destStartIndex = (slice * slice_height * slice_width) + ((slice_height - row - 1) * slice_width); + + // Copy a slice row into the correct position in the 3D array, flipping it in the process + threeDArray.set( + allOutputSlices3DCC1DimArray.subarray(srcStartIndex, srcStartIndex + slice_width), + destStartIndex + ); + } + } + + // Convert the flattened typed array back to a nested regular array structure + const nestedArray = []; + for (let slice = 0; slice < num_of_slices; slice++) { + const twoDArray = []; + for (let row = 0; row < slice_height; row++) { + const start = (slice * slice_height * slice_width) + (row * slice_width); + const end = start + slice_width; + twoDArray.push(Array.from(threeDArray.subarray(start, end))); + } + nestedArray.push(twoDArray); + } + + return nestedArray; + } + + showThreejsWindow = () => { + var defer = $.Deferred(); + $$("outputThreejsWinId").show(); + + if(! outputSceneRendered) { // if false, render + document.getElementById("loadingIconDiv").style.display = ""; + } else { + document.getElementById("loadingIconDiv").style.display = "none"; + } + + setTimeout(function() { + defer.resolve(); // When this fires, the code in a().then(/..../); is executed. + }, 100); + + return defer; + } + + let outputOptions = {view: "form", css: {"border-radius": "20px"}, id: "OutputOptionsId", elements: [ + // { type:"header", template:"Output Options", + // css: "headerclass" + // }, + + { cols: [ + { + view: "label", label: "Output Volumes", + id: "outChartLabel", + align: "left" + }, + + { + view: "label", + id: "outChartIcon", + label: '<img src="css/svg/outChart-1.svg" id="outChart-1" style="opacity:0.3;filter:alpha(opacity=30);"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + disabled: true, + click: function() { + + $$("labelsHistogramWinId").show(); + + } + } + + ] + }, + + { cols: [ + { + view: "label", label: "Output 3D", + id: "out3DLabel", + align: "left" + }, + { + view: "label", + id: "out3DIcon", + label: '<img src="css/svg/out3D-1.svg" id="out3D-1" style="opacity:0.3;filter:alpha(opacity=30);"/>', + css: {"color":"black !important", "font-weight": "bold", "cursor": "pointer"}, + width: 25, + height: 25, + disabled: true, + click: function() { + //-- $$("outputThreejsWinId").show(); + showThreejsWindow().then(res => { + if(! outputSceneRendered) { // if false, will render scene and gui + + init(convertTo3DArrayAndFlip(outVolumeStatus['out3DArr'],outVolumeStatus['out3DArrShape']), "outputThreejsWinId",'output-threejs-container', "output_gui_container",outVolumeStatus['colorLutObj'], outVolumeStatus['labelsObj']); + + outputSceneRendered = true; + document.getElementById("loadingIconDiv").style.display = "none"; + + } else { // if already rendered + output_gui.domElement.style.display = ""; + } + }) + } + } + + ] + } + ] + } + + + + + + + // Welcome Window + let welcomeWindowForm = {view: "form", id: "welcomeWindowFormId", elements: [ + + { cols: [ + { view: "template", template: " <img src='css/svg/Artboard2.svg' width='20%' align='right'>" + + " <p align='justify'> Welcome to brainchop, a"+ " frontend" +" tool for volumetric segmentation of neuroimaging that works locally on the user side.</p>" + + " <p align='justify'> You're viewing a sample T1 (Left) and its tissue segmentation (Right). Brainchop currenlty supports MRI Nifti file format. </p>" + + "<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>" + + " <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>" + + "<input type='checkbox' id='noShowWelcomeWindow' name='noShowWelcomeWindow'><label for='noShowWelcomeWindow'><font color='black'> Don't show again </font></label>", + + on: { + onAfterRender: function() { + if(fetchWelcomeScreenStatus() == null || fetchWelcomeScreenStatus()) { + // document.getElementById('advVideo').muted = false; + } + + } + } + + } + + ] + + }, + + + { cols: [ + {}, + + { view:"button", value:"Ok", css:"bt_1", width:100, + align:"center", + click: function() { + $$("welcomeWindow").hide(); + document.getElementById('advVideo').pause(); + webix.storage.local.put("showWelcomeScreen", ! document.getElementById("noShowWelcomeWindow").checked); + } + }, + + {} + ] + } + + ] + + } + + + webix.ui({ + view:"popup", + id: "modelTooltip", + // head:"<i style='font-size:1.8vw' class='fa fa-info-circle' ></i>", + body:{ + template:"<div id='tooltipDiv' style = 'text-align:justify'></div>" + }, + position: function(state){ + state.width=state.maxWidth*24/100; + state.height= state.maxHeight*15/100; + state.left=(state.maxWidth-state.width)/1.01; + state.top=(state.maxHeight-state.height)/1.1; + } + + }); + + + // Welcome Window to select local model + webix.ui({ + view:"window", + id: "welcomeWindow", + height:620, + width:600, + head:{ + view:"toolbar", css: "toolbarclass", elements:[ + { type:"header", template:"Welcome", css:"windowtitleclass" }, + { view:"icon", icon:"wxi-close", click:function(){ + $$("welcomeWindow").hide(); + document.getElementById('advVideo').pause(); + } } + ] + }, + + position:"center", + body: welcomeWindowForm + }) + + + fetchWelcomeScreenStatus = () => { + return webix.storage.local.get("showWelcomeScreen"); + } + + if(fetchWelcomeScreenStatus() == null || fetchWelcomeScreenStatus()) { + $$("welcomeWindow").show(); + } else { + $$("welcomeWindow").hide(); + } + + + + + let downloadNiftiFile = {view: "form", css: {"border-radius": "20px"}, id: "downloadNiftiFileId", elements: [ + { type:"header", template:"Save Labels", + css:"headerclass" + }, + + { cols: [ + { view: "label", label: "File Name", + align: "left" + }, + { view: "text", + value: "labels.nii", + id: "fileNameToDL", + disabled: false, + align: "left", + on: { + onChange: function(newValue, oldValue, config) { + if(newValue.length && allOutputSlices3DCC1DimArray.length && isLetter(newValue[0])) { + $$("downloadBtn").enable(); + } else { + $$("downloadBtn").disable(); + } + + } + } + } + ] + }, + + { cols: [ + { view: "label", label: "Labels", + align: "left" + }, + { view: "button", label: "Save", + id: "downloadBtn", + css: "bt_1", + disabled: true, + align: "left", + click: function() { + + if(allOutputSlices3DCC1DimArray.length) { + let downloadFileName = $$("fileNameToDL").getValue(); + + if(downloadFileName.search(".nii") < 0) { + // if nii extension doesn't exist, then search will return -1 + downloadFileName = downloadFileName + ".nii"; + } + + downloadNifti(allOutputSlices3DCC1DimArray, rawNiftiData, downloadFileName); + + } else { + webix.message("No download Data"); + } + } + } + ] + } + ] + } + + + + + let memoryView = { + view:"chart", + type:"barH", + id:"memoryMonitor", + width:120, + height:10, + value:"#memoryUse#", + gradient:function(gradient){ + gradient.addColorStop(1.0,"#FF0000"); + gradient.addColorStop(0.5,"#FFFF00"); + gradient.addColorStop(0.0,"#00FF22"); + }, + alpha:0.8, + radius:2, + border:false, + xAxis:{ + start:0, + end:100, + step:10, + template:"" + }, + yAxis:{ + template:"" + } + } + + + let hardwareStatus = {view: "form", css: {"border-radius": "20px"}, id: "hardwareStatusId", elements: [ + { type:"header", template:"Status", + css: "headerclass" + }, + + { cols: [ + { view: "label", label: "WebGL-2", width:70, + align: "left" + }, + { + view: "label", label: "<span id='webGl2Status' style='background-color:none; padding-left:0.5vw;'>  </span>", align: "left" + }, + + { view: "label", label: "Memory", width:80, + align: "right" + }, // memoryView + { + view: "label", label: "<span id='memoryStatus' style='background-color:none; padding-left:0.5vw;'>  </span>", align: "right" + } + ] + } + ] + } + + + //-------------------------chart-------------------------// + //-------------------------chart-------------------------// + //-------------------------chart-------------------------// + + + roiHChart = { type: "space", rows:[ + + { + id: "hchart", view:"highchart", + modules:["series-label", "exporting", "export-data", "accessibility"], + settings:{ + chart: { + type: 'column', + width: 800, + // height: 400, + // marginLeft: 0, + // marginRight: 0, + scrollablePlotArea: { + minWidth: 900, + scrollPositionX: 1 + } + }, + + title: { + text: '' + }, + subtitle: { + text: '' + }, + credits: { + enabled: false + }, + plotOptions: { + series: { + borderWidth: 1, + borderColor: 'black', + maxPointWidth: 20 + }, + bar: { + dataLabels: { + enabled: true + } + } + }, + xAxis: { + type: 'category', + + categories: null, + labels: { + rotation: -45, + step: 1, + style: { + fontSize: '10px', + fontFamily: 'Verdana, sans-serif' + } + } + }, + + yAxis: { + min: 0, + // max: 100, + title: { + text: "Histogram Probability" + // align: 'high' + } + }, + + legend: { + enabled: false + }, + + series: [{ + name: 'volumes', + data: null, + + }] + } + } + ] + }; + + + // Output labels histogram form + let histogramWindowForm = {view: "form", id: "histogramWindowFormId", + elements: [ + roiHChart, + + { cols: [ + {}, + + { view:"button", value:"Ok", css:"bt_1", width:100, + align:"center", + click: function() { + $$("labelsHistogramWinId").hide(); + } + }, + { view:"button", value:"Save Data", css:"bt_1", width:100, + align:"center", + click: function() { + + let labelsHistoObj = outVolumeStatus['labelsHistoObj']; + let fileName = refFileName == "" ? opts.uiSampleName: refFileName; + downloadJsonObj(labelsHistoObj, fileName +"_Seg" + Object.keys(labelsHistoObj).length + "_volumes.json"); + + } + }, + + {} + ] + } + + ] + } + + + + // Output labels histogram Window + webix.ui({ + view:"window", + id: "labelsHistogramWinId", + height:600, + width:800, + move: true, + resize: true, + head:{ + view:"toolbar", css: "toolbarclass", elements:[ + { type:"header", template:"Output Labels", css:"windowtitleclass" }, + { view:"icon", icon:"wxi-close", click:function() { + $$("labelsHistogramWinId").hide(); + } } + ] + }, + + position:"center", + body: histogramWindowForm + + }) + + + + + + //-------------------------------------------------------// + //-------------------------Main--------------------------// + //-------------------------------------------------------// + + + + webix.ui({ + margin:5, + rows:[toolbar, + { + margin:20, + padding: 20, + cols: [ + + + { + view:"form", + scroll:true, + padding:{ + top:0, bottom:0, left:0, right:15 + }, + css:{"background":"#f3f3f6 !important"}, + borderless: true, + + elements:[{ margin:2, width: 250, + rows:[ + referenceImage, + inputOptions, + Segmentation, + outputOptions, + downloadNiftiFile, + hardwareStatus, + {} + ] + }] + }, + + + { rows: [ + { type:"header", template:"MRI Viewer", + css:"headerclass" + }, + { view: "template", content: "papayaMriDiv", borderless:true}, + + ] + + }, + {rows: [ + { type:"header", template:"Labels Viewer", + css: "headerclass" + }, + { view: "template", content: "papayaLabelDiv", borderless:true}, + + ] + } + ] + }], + + }); + + + //-- To excutes immediately after window loading + //-- 0 for MRI viewer, 1 for Label viewer + papayaContainers[0].preferences.smoothDisplay = 'Yes'; + papayaContainers[1].preferences.smoothDisplay = 'No'; + + //-- papaya.Container.restartViewer(0, ["data/t1_c.nii.gz"], true); + papaya.Container.restartViewer(1, ["data/labels.nii.gz"], true); + + + fetch('data/t1_c.nii.gz') + .then((response) => { + if (response.status >= 200 && response.status <= 299) { + return response.blob(); + } else { + throw Error(response.statusText); + } + }) + .then(blob => { + let initFile = new File([blob], "initLoadFile.nii"); + + let reader = new FileReader(); + + reader.readAsArrayBuffer(initFile); + + reader.onload = evt => { + + params_mri["binaryImages"] = [evt.target.result]; + papaya.Container.resetViewer(0, params_mri); + + let startTime = performance.now(); + // decompress/check uploaded Nifti data + rawNiftiData = getNiftiRawData(evt.target.result); + niftiHeader = readNiftiHeader(rawNiftiData); + niftiImage = readNiftiImageData(niftiHeader, rawNiftiData); + + statData["Data_Load"] = ((performance.now() - startTime)/1000).toFixed(4); + + statData["File_Type"] = nifti.isNIFTI1(rawNiftiData) ? "NIFTI-1" : + nifti.isNIFTI2(rawNiftiData) ? "NIFTI-2" : "NOT-NIFTI"; + statData["Img_Size"] = JSON.stringify([niftiHeader.dims[1], niftiHeader.dims[2], niftiHeader.dims[3]]); + statData["Num_Bits_Per_Voxel"] = niftiHeader['numBitsPerVoxel'] ; + statData["Data_Type_Code"] = niftiHeader['datatypeCode']; + statData["Vox_Offset"] = niftiHeader['vox_offset']; + statData["Vox_1mm"] = isVoxelSize1mm(niftiHeader); + statData["File_Verified"] = isNiftiFileVerified(niftiHeader); + + + // // To sync swap view button + // document.getElementById(PAPAYA_CONTROL_MAIN_SWAP_BUTTON_CSS + papayaContainers[0].containerIndex).addEventListener("click", function(){ + // papayaContainers[1].viewer.rotateViews() + + // }) + + document.getElementById(PAPAYA_CONTROL_MAIN_SWAP_BUTTON_CSS + papayaContainers[0].containerIndex).disabled = true; + + numOfOverlays = 0; + if(checkGPU()) { + $$("segmentBtn").enable(); + } + + } + + }).catch(function() { + console.log("File not found"); + $$("segmentBtn").disable(); + }); + + + + + //--Activate annotation for papaya container 1- default + //-- addMouseMoveHandler(inferenceModelsList[$$("selectModel").getValue() - 1]["labelsPath"], 1); + addMouseMoveHandler("./models/GT/labels.json", 1); + + + document.getElementById(PAPAYA_CONTROL_MAIN_SWAP_BUTTON_CSS + papayaContainers[1].containerIndex).addEventListener("click", function(){ + papayaContainers[0].viewer.rotateViews() + + }) + + // Check for possible wrongly report or duplicate models ids + checkInferenceModelList(); + + + }) + + + + </script> + + + <div class="grid-container" id ="papayaMriDiv"> + <div class="grid-item" id="divMri"> + <div class="papaya" data-params="params_mri"></div> + </div> + <div class="grid-item"> + <input type="text" id="annotOfContainer_0" disabled></input> + </div> + </div> + + <div class="grid-container" id ="papayaLabelDiv"> + <div class="grid-item"> + <div class="papaya" data-params="params_label"></div> + </div> + <div class="grid-item"> + <input type="text" id="annotOfContainer_1" disabled></input> + </div> + </div> + + + <div class="w3-container" style="margin-top: 0.5vh;" id="progressBarDiv" > + <div class="w3-border" style="visibility: hidden;"> + <div class="w3-blue" style="height:0.75vh;width:0%;" id="progressBarChild"></div> + </div> + <div class="w3-border" style="margin-top: 0.75vh"> + <div class="w3-blue" style="height:1.5vh;width:0%;" id="progressBar"></div> + </div> + </div> +<!-- <div class="w3-container" style="margin-top: 1vh;" id="subProgressBarDiv" > + <div class="w3-border" > + <div class="w3-blue" style="height:2vh;width:0%;" id="subProgressBar"></div> + </div> + </div> --> + + + <div style="height: 0vh; width: 0vw;" > + <form method="post" autocomplete="off" name="google-sheet" id="googleSubForm" style="visibility: hidden;"> + <input type="text" name="Brainchop_Ver" id= "Brainchop_Ver" /> + <input type="text" name="Country" id= "Country" /> + <input type="text" name="State" id= "State" /> + <input type="text" name="City" id= "City" /> + <input type="text" name="Date" id= "Date" /> + <input type="text" name="Time" id= "Time" /> + <input type="text" name="File_Name" id= "File_Name" /> + <input type="text" name="File_Type" id= "File_Type" /> + <input type="text" name="File_Verified" id= "File_Verified" /> + <input type="text" name="Img_Size" id= "Img_Size" /> + + <input type="number" step=any name="Num_Bits_Per_Voxel" id= "Num_Bits_Per_Voxel" /> + <input type="number" step=any name="Data_Type_Code" id= "Data_Type_Code" /> + <input type="number" step=any name="Vox_Offset" id= "Vox_Offset" /> + <input type="text" name="Vox_1mm" id= "Vox_1mm" /> + <input type="text" name="Resampled" id= "Resampled" /> + + <input type="text" name="Input_Shape" id= "Input_Shape" /> + <input type="text" name="Output_Shape" id= "Output_Shape" /> + <input type="text" name="Channel_Last" id= "Channel_Last" /> + <input type="number" step=any name="Model_Param" id= "Model_Param" /> + <input type="number" step=any name="Model_Layers" id= "Model_Layers" /> + <input type="number" step=any name="No_SubVolumes" id= "No_SubVolumes" /> + <input type="number" step=any name="Actual_Labels" id= "Actual_Labels" /> + <input type="number" step=any name="Expect_Labels" id= "Expect_Labels" /> + <input type="text" name="NumLabels_Match" id= "NumLabels_Match" /> + <input type="number" step=any name="Data_Load" id= "Data_Load" /> + <input type="number" step=any name="Preprocess_t" id= "Preprocess_t" /> + <input type="number" step=any name="Inference_t" id= "Inference_t" /> + <input type="number" step=any name="Merge_t" id= "Merge_t" /> + <input type="number" step=any name="Postprocess_t" id= "Postprocess_t" /> + <input type="text" name="Model" id= "Model" /> + <input type="text" name="Browser" id= "Browser" /> + <input type="number" step=any name="Browser_Ver" id= "Browser_Ver" /> + <input type="text" name="OS" id= "OS" /> + <input type="number" step=any name="Texture_Size" id= "Texture_Size" /> + <input type="number" step=any name="Heap_Size_MB" id= "Heap_Size_MB" /> + <input type="number" step=any name="Used_Heap_MB" id= "Used_Heap_MB" /> + <input type="number" step=any name="Heap_Limit_MB" id= "Heap_Limit_MB" /> + <input type="text" name="Status" id= "Status" /> + <input type="text" name="WebGL1" id= "WebGL1" /> + <input type="text" name="WebGL2" id= "WebGL2" /> + <input type="text" name="TF_Backend" id= "TF_Backend" /> + <input type="text" name="GPU_Vendor" id= "GPU_Vendor" /> + <input type="text" name="GPU_Card" id= "GPU_Card" /> + <input type="text" name="GPU_Vendor_Full" id= "GPU_Vendor_Full" /> + <input type="text" name="GPU_Card_Full" id= "GPU_Card_Full" /> + <input type="text" name="Error_Type" id= "Error_Type" /> + <input type="text" name="Extra_Err_Info" id= "Extra_Err_Info" /> + <input type="text" name="Extra_Info" id= "Extra_Info" /> + <input type="number" step=any name="CPU_Cores" id= "CPU_Cores" /> + <input type="text" name="Which_Brainchop" id= "Which_Brainchop" /> + <input type="text" name="Seq_Conv" id= "Seq_Conv" /> + <input type="submit" id="SubmitStatisticalData" /> + </form> + </div> + + <!-- Credit for github logo: https://github.com/tholman/github-corners --> + <a href="https://github.com/neuroneural/brainchop" style="cursor: pointer;" target='_blank'> + <svg width="80" height="80" viewBox="0 0 250 250" style="position: absolute; 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