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motion.html
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<!DOCTYPE html>
<html>
<head>
<title>Report on fMRI motion levels</title>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no" />
<!-- General styles for the dashboard -->
<link rel="stylesheet" type="text/css" href="assets/general/css/qc_dash.css" />
<!-- Custom style sheet for motion report -->
<link rel="stylesheet" type="text/css" href="assets/motion/css/motion.css" />
<!-- Bootstrap -->
<link rel="stylesheet" type="text/css" href="lib/bootstrap/bootstrap.min.css" />
<!-- Keen.io -->
<link rel="stylesheet" type="text/css" href="lib/keen/keen-dashboards.css" />
<!-- Select 2 -->
<link href="lib/select2/select2.min.css" rel="stylesheet" type="text/css" />
<!-- c3.js -->
<link href="lib/c3js/c3.min.css" rel="stylesheet" type="text/css" />
</head>
<body class="application">
<!-- Navbar -->
<div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<div class="container-fluid">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="https://dashqc-fmri.readthedocs.io/en/latest/index.html">dashQC_fmri</a>
</div>
<div class="navbar-collapse collapse">
<ul class="nav navbar-nav navbar-left">
<li class="navbar_item"><a href="index.html">Summary</a></li>
<li class="navbar_item"><a href="registration.html">Registration</a></li>
<li class="navbar_item navbar-brand-current"><a href="motion.html">Motion</a></li>
</ul>
</div>
</div>
</div>
<!-- Contents -->
<div class="container-fluid">
<div class="row">
<!-- Frame displacement plots -->
<div class="col-sm-6">
<div class="chart-wrapper">
<div class="chart-title">Frame displacement</div>
<div class="chart-stage">
<div id="chartFd"></div>
</div>
<div class="chart-notes">
Click to select a time point. Mouse scroll to zoom.
</div>
</div>
</div>
<!-- Motion visualizer in native space -->
<div class="col-sm-6">
<div class="chart-wrapper">
<div class="chart-title">
fMRI time frames in native space. Select a run:
<select id="select-BOLD" style="width: 50%"></select>
</div>
<div class="chart-stage" id="motionNative">
<img class="sliderNext" src="lib/jsImageSlider/navbuttons.png" />
<img class="sliderPrev" src="lib/jsImageSlider/navbuttons.png" />
<canvas id="sliderNative" />
<!-- <img id="spriteNative" class="hidden" src="assets/motion/images/target_native_sub0050784_session1_rest.png" /> -->
<!-- <img id="spriteNative" class="hidden" src="assets/motion/images/static_figure.png" /> -->
</div>
<div class="chart-notes">
Click the left/right arrows to go forward/backward in time.
</div>
</div>
</div>
</div>
<div class="row">
<!-- Translation parameters plots -->
<div class="col-sm-6">
<div class="chart-wrapper">
<div class="chart-title">Translation parameters</div>
<div class="chart-stage">
<div id="chartTsl"></div>
</div>
<div class="chart-notes">
Click to select a time point. Mouse scroll to zoom.
</div>
</div>
</div>
<!-- Motion visualizer in stereotaxic space -->
<div class="col-sm-6">
<div class="chart-wrapper">
<div class="chart-title">fMRI time frames in stereotaxic space</div>
<div class="chart-stage" id="motionStereo">
<img class="sliderNext" src="lib/jsImageSlider/navbuttons.png" />
<img class="sliderPrev" src="lib/jsImageSlider/navbuttons.png" />
<canvas id="sliderStereo" />
<!-- <img id="spriteStereo" class="hidden" src="assets/motion/images/motion_stereo_sub0050784_session1_rest.png" /> -->
</div>
<div class="chart-notes">
Click the left/right arrows to go forward/backward in time.
</div>
</div>
</div>
</div>
<div class="row">
<!-- Rotation parameters plots -->
<div class="col-sm-6">
<div class="chart-wrapper">
<div class="chart-title">Rotation parameters</div>
<div class="chart-stage">
<div id="chartRot" style="width:100%"></div>
</div>
<div class="chart-notes">
Click to select a time point. Mouse scroll to zoom.
</div>
</div>
</div>
<!-- Registration with the session/run of reference -->
<div class="col-sm-6">
<div class="chart-wrapper">
<div class="chart-title">Run vs Reference volume</div>
<div class="chart-stage" id="runVReference" style="background-color:white !important;">
<div id="divRegistration" class="register">
</div>
</div>
<div class="chart-notes">
Hover the mouse over to switch between images.
</div>
</div>
</div>
</div>
</div>
<hr />
<!-- Footer -->
<footer class="footer">
<div class="container-fluid">
<div class="row">
<div class="col-sm-12">
<p class="small text-muted">Dashboard built with ♥ by <a href="http://simexp-lab.org">SIMEXP Lab.</a></p>
</div>
</div>
</div>
</footer>
<!-- Dependencies -->
<!-- D3 and C3 -->
<script src="lib/d3js/d3.min.js" charset="utf-8"></script>
<script src="lib/c3js/c3.min.js"></script></head>
<!-- jQuery -->
<script type="text/javascript" src="lib/jquery/jquery.min.js"></script>
<!-- For bootstrap -->
<script type="text/javascript" src="lib/bootstrap/bootstrap.min.js"></script>
<!-- For keen.io -->
<script type="text/javascript" src="lib/keen/keen.min.js"></script>
<!-- For select 2 -->
<script type="text/javascript" src="lib/select2/select2.min.js"></script>
<!-- Required data from pipeline processing script -->
<!-- List of available runs -->
<script type="text/javascript" src="assets/group/js/listRun.js"></script>
<!-- Data for chartFD and chartNbVol -->
<script type="text/javascript" src="assets/summary/js/fd.js"></script>
<!-- Custom dashQC JS -->
<!-- QC Dashboard Objects -->
<script type="text/javascript" src="assets/general/js/qc_dash_objects.js"></script>
<script>
// I. Declarations //
// Modular asset naming
var fileAffixes = {
"target": {
"prefix": {
"native": "target_native_",
"stereo": "target_stereo_",
},
"suffix": {
"native": "_rest",
"stereo": "_rest",
},
},
"motion": {
"prefix": {
"native": "motion_native_",
"stereo": "motion_stereo_",
},
"suffix": {
"native": "_rest",
"stereo": "_rest",
},
},
};
// Constants
var numFrame = 0; // Initially display the first time frame
var percVisu = 0.7; // The BOLD montage use 70% of the window
var percVisuStr = (100 * percVisu).toString() + "%";
var imageLoadPromises = { spriteNative: null, spriteStereo: null, registration: null };
// Globals
// Spacers
var spacerNative = null;
var spacerStereo = null;
// Charts
var chartTsl = null;
var chartRot = null;
var chartFd = null;
// Run data
var runID = "";
var runData = null;
// Experimental flags
var drawWithGrid = false;
// function imagePromise(src) {
// var deferred = $.Deferred();
// var img = new Image();
// function resolve() {
// // Resolution callbacks receive the image, which you can then inject into the DOM
// // to avoid triggering an extra HTTP request in IE
// return deferred.resolve(img);
// }
// // Resolution events
// $( img ).on( {
// error : deferred.reject,
// load : resolve
// } );
// // Attach the source afterwards, since DOM synchronicity is weird:
// // A cached image will sometimes load or error on assignment
// img.src = src;
// // ...But sometimes cached images never fire load!
// // In this case they would already be in the DOM at this point. We need to infer it:
// if ( img.complete && img.naturalWidth !== undefined ) {
// // And then use setTimeout to resolve asynchronously (otherwise promise is broken!)
// setTimeout( resolve );
// };
// return deferred.promise();
// }
// function loadImage(image) {
// if ( !image ) {
// return Promise.reject();
// } else if (typeof image === 'string') {
// /* Create a <img> from a string */
// const src = image;
// image = new Image();
// image.src = src;
// } else if (image.length !== undefined) {
// /* Treat as multiple images */
// // Momentarily ignore errors
// const reflected = [].map.call(image, img => load(img).catch(err => err));
// return Promise.all(reflected).then(results => {
// const loaded = results.filter(x => x.naturalWidth);
// if (loaded.length === results.length) {
// return loaded;
// }
// return Promise.reject({
// loaded,
// errored: results.filter(x => !x.naturalWidth)
// });
// });
// } else if (image.tagName !== 'IMG') {
// return Promise.reject();
// }
// const promise = new Promise((resolve, reject) => {
// if (image.naturalWidth) {
// // If the browser can determine the naturalWidth the
// // image is already loaded successfully
// resolve(image);
// } else if (image.complete) {
// // If the image is complete but the naturalWidth is 0px
// // it is probably broken
// reject(image);
// } else {
// image.addEventListener('load', fullfill);
// image.addEventListener('error', fullfill);
// }
// function fullfill() {
// if (image.naturalWidth) {
// resolve(image);
// } else {
// reject(image);
// }
// image.removeEventListener('load', fullfill);
// image.removeEventListener('error', fullfill);
// }
// });
// promise.image = image;
// return promise;
// }
// Main drawing function
function drawCharts(p_runID) {
// 1. Load spacer images, to set the size of a montage in each mosaic
spacerNative = new Image();
if ( drawWithGrid ) {
spacerNative.src = "assets/motion/images/" + "static_figure.png";
} else {
spacerNative.src = "assets/motion/images/" + fileAffixes.target.prefix.native +
p_runID + ".png";
}
spacerStereo = new Image();
spacerStereo.src = "assets/motion/images/" + fileAffixes.target.prefix.stereo +
p_runID + ".png";
// 2. Change img src values and create promises to detect when they finish loading
if ( drawWithGrid ) {
$("#spriteNative").attr("src", "assets/motion/images/" + "small_grid_figure.png");
} else {
$("#spriteNative").attr("src", "assets/motion/images/" +
fileAffixes.motion.prefix.native + p_runID + ".png");
}
// imageLoadPromises.spriteNative = $("#spriteNative").load().promise();
$("#spriteStereo").attr("src", "assets/motion/images/" +
fileAffixes.motion.prefix.stereo + p_runID + ".png");
// imageLoadPromises.spriteStereo = $("#spriteStereo").load().promise();
$("#registration").attr("src", "assets/motion/images/" +
fileAffixes.target.prefix.stereo + p_runID + ".png");
// imageLoadPromises.registration = $("#registration").load().promise();
// c3.js data for the translation, rotation, and FD parameters charts
// chartTsl = new QCDash_LineChart(tsl, "chartTsl", "Time (TRs)", "Translation (mm)");
// chartTsl.generate();
// chartRot = new QCDash_LineChart(rot, "chartRot", "Time (TRs)", "Rotation (degrees))");
// chartRot.generate();
// chartFd = new QCDash_LineChart(fd, "chartFd", "Time (TRs)", "Frame displacement (pseudo mm))");
// chartFd.generate();
var imgsLoaded = { spriteNative: false, spriteStereo: false, registration: false };
$("#spriteNative").on("load", function() {
imgsLoaded.spriteNative = true;
if ( imgsLoaded.spriteNative && imgsLoaded.spriteStereo && imgsLoaded.registration ) {
imgsLoaded.spriteNative = imgsLoaded.spriteStereo = imgsLoaded.registration = false;
finishDrawCharts(p_runID);
}
});
$("#spriteStereo").on("load", function() {
imgsLoaded.spriteStereo = true;
if ( imgsLoaded.spriteNative && imgsLoaded.spriteStereo && imgsLoaded.registration ) {
imgsLoaded.spriteNative = imgsLoaded.spriteStereo = imgsLoaded.registration = false;
finishDrawCharts(p_runID);
}
});
$("#registration").on("load", function() {
imgsLoaded.registration = true;
if ( imgsLoaded.spriteNative && imgsLoaded.spriteStereo && imgsLoaded.registration ) {
imgsLoaded.spriteNative = imgsLoaded.spriteStereo = imgsLoaded.registration = false;
finishDrawCharts(p_runID);
}
});
// Make sure images are loaded before proceeding with the rest of drawCharts
// imagePromise($("#spriteNative").attr("src")).then(function() {
// $.when(imageLoadPromises.spriteNative,
// imageLoadPromises.spriteStereo,
// imageLoadPromises.registration).then(function() {
// console.log("Promises fulfilled!");
// // Trigger the building of motion movies
// selectTime(0);
// // Set the size of the registration figure in tune with motion movies
// // $("#registration").width(myPercVisuStr);
// // Add background image with correct size in the registration figure
// figRegistration = $("#divRegistration");
// figRegistration.css("backgroundImage",
// "url('assets/motion/images/" + fileAffixes.target.prefix.stereo +
// p_runID + ".png')");
// figRegistration.css("backgroundSize", myPercVisuStr);
// figRegistration.css("backgroundPosition", "center");
// figRegistration.css("backgroundRepeat", "no-repeat");
// // Resize the rotation chart, which is not tweaked by selectTime
// // (unlike the FD and translation charts)
// chartRot.m_chartRef.resize({ height: $("#registration").height() });
// }
// );
}
function finishDrawCharts(p_runID) {
chartTsl = new QCDash_LineChart(tsl, "chartTsl", "Time (TRs)", "Translation (mm)");
chartTsl.generate();
chartRot = new QCDash_LineChart(rot, "chartRot", "Time (TRs)", "Rotation (degrees)");
chartRot.generate();
chartFd = new QCDash_LineChart(fd, "chartFd", "Time (TRs)", "Frame displacement (pseudo mm))");
chartFd.generate();
// Trigger the building of motion movies
selectTime(0);
// Set the size of the registration figure in tune with motion movies
$("#registration").width(percVisuStr);
// Add background image with correct size in the registration figure
figRegistration = $("#divRegistration");
figRegistration.css("backgroundImage",
"url('assets/motion/images/" + fileAffixes.target.prefix.stereo +
p_runID + ".png')");
figRegistration.css("backgroundSize", percVisuStr);
figRegistration.css("backgroundPosition", "center");
figRegistration.css("backgroundRepeat", "no-repeat");
// Resize the rotation chart, which is not tweaked by selectTime
// (unlike the FD and translation charts)
chartRot.m_chartRef.resize({ height: $("#registration").height() });
}
// II. Utility functions
// Function to draw volumes for a particular time frame.
// Update canvas based on two big mosaic files
// Native: images in native space, prior to motion correction
// Stereo: images in stereostaxic space, after motion correction
function drawMotion(p_frame, p_type) {
var canvas = document.getElementById("slider" + p_type);
var wImg = $("#slider" + p_type).parent().width();
var wSpacer = { Native: spacerNative.width, Stereo: spacerStereo.width };
var hSpacer = { Native: spacerNative.height, Stereo: spacerStereo.height };
var nbTimeFrames = Math.floor((document.getElementById("spriteStereo").width / wSpacer.Native) - 1);
var rSpacer = hSpacer[p_type] / wSpacer[p_type];
var hImg = Math.round(wImg * percVisu * rSpacer);
// Get number of time frames
if ( canvas.width != wImg ) {
canvas.width = wImg;
canvas.height = hImg;
}
var ctx = canvas.getContext("2d");
ctx.clearRect(0, 0, canvas.width, canvas.height);
ctx.drawImage(document.getElementById("sprite" + p_type),
p_frame * wSpacer[p_type],
0,
wSpacer[p_type],
hSpacer[p_type],
wImg * (1 - percVisu) / 2,
0,
wImg * percVisu,
hImg);
ctx.fillStyle = "#ffffff";
ctx.fillText("Frame number " + p_frame + "/" + nbTimeFrames,
wImg * 1.2 * (1 - percVisu) / 2,
0.05 * hImg);
numFrame = p_frame;
return hImg;
}
// Find run ID number in provided data given a run name
function findRunIDFromName(p_data, p_run) {
let foundID = null;
for ( let index = 0; index < p_data.length; index++ ) {
if ( p_data[index].text === p_run ) {
foundID = p_data[index].id;
break;
}
}
return foundID;
}
// Function to parse the page parameters
function getParameterByName(p_name, p_url) {
if ( !p_url ) {
p_url = window.location.href;
}
p_name = p_name.replace(/[\[\]]/g, "\\$&");
var regex = new RegExp("[?&]" + p_name + "(=([^&#]*)|&|#|$)"),
results = regex.exec(p_url);
if ( !results ) {
return null;
}
if ( !results[2] ) {
return '';
}
return decodeURIComponent(results[2].replace(/\+/g, " "));
}
// Creates links to motion report attached to the bars in chartMotion chartBrain and chartIntra
function selectRun(d, chart) {
run = chart.internal.config.axis_x_categories[d.x];
var win = window.open(["motion_report_" + run + ".html"], "_blank");
if ( win ) {
// Browser has allowed it to be opened
win.focus();
} else {
// Browser has blocked it
alert("Please allow popups for this website");
}
}
// Function to select a time frame. It calls the drawing of canvas,
// select the correct time point in the graphs, and also resize
// the translation and rotation graphs based on the corresponding movies.
function selectTime(p_frame) {
var hImgNative = null;
if ( drawWithGrid ) {
hImgNative = drawMotion_Grid(p_frame, "Native");
} else {
hImgNative = drawMotion(p_frame, "Native");
}
if ( $("#chartFd").height() != hImgNative ) {
chartFd.m_chartRef.resize({ height: hImgNative });
}
let hImgStereo = drawMotion(p_frame, "Stereo");
if ( $("#chartTsl").height() != hImgStereo ) {
chartTsl.m_chartRef.resize({ height: hImgStereo });
}
chartTsl.m_chartRef.select(["motion_tx" , "motion_ty" , "motion_tz"], [p_frame], true);
chartRot.m_chartRef.select(["motion_rx" , "motion_ry" , "motion_rz"], [p_frame], true);
chartFd.m_chartRef.select(["FD" , "scrub" ], [p_frame], true);
}
// Function to move forward by one time sample
function nextTime() {
var nextFrame = numFrame + 1;
// Get number of time frames
var nbTimeFrames = ((document.getElementById("spriteNative").width / spacerNative.width) *
(document.getElementById("spriteNative").height / spacerNative.height)) - 1;
if ( nextFrame > nbTimeFrames ) {
return;
} else {
selectTime(nextFrame);
}
}
// Function to move back by one time sample
function prevTime() {
prevFrame = numFrame - 1;
if ( prevFrame < 0 ) {
return;
} else {
selectTime(prevFrame);
}
}
// Grid solution for frame drawing
function drawMotion_Grid(frame, type) {
var canvas = document.getElementById("slider" + type);
var wImg = $("#slider" + type).parent().width();
var wSpacer = { Native: spacerNative.width, Stereo: spacerStereo.width };
var hSpacer = { Native: spacerNative.height, Stereo: spacerStereo.height };
var imageGridDims = { rows: Math.floor(document.getElementById("spriteNative").height / hSpacer.Native),
columns: Math.floor(document.getElementById("spriteNative").width / wSpacer.Native) };
var nbTimeFrames = Math.floor((imageGridDims.rows * imageGridDims.columns) - 1);
var rSpacer = hSpacer[type] / wSpacer[type];
var hImg = Math.round(wImg * percVisu * rSpacer);
// Get number of time frames
if ( canvas.width != wImg ) {
canvas.width = wImg;
canvas.height = hImg;
}
var ctx = canvas.getContext("2d");
var currentRow = Math.floor(frame / imageGridDims.columns);
// console.log("Drawing frame: " + frame.toString() + " for current row: " + currentRow.toString());
// console.log("\tat (" + ((frame / (currentRow + 1)) * wSpacer[type]).toString() + "," + (currentRow * hImg).toString() + ")")
ctx.clearRect(0, 0, canvas.width, canvas.height);
ctx.drawImage(document.getElementById("sprite" + type),
(frame / (currentRow + 1)) * wSpacer[type],
currentRow * hImg,
wSpacer[type],
hSpacer[type],
wImg * (1 - percVisu) / 2,
0,
wImg * percVisu,
hImg);
ctx.fillStyle = "#ffffff";
ctx.fillText("Frame number " + frame + "/" + nbTimeFrames,
wImg * 1.2 * (1 - percVisu) / 2,
0.05 * hImg);
numFrame = frame;
return hImg;
}
// III. Events //
// Associate the arrows of the slider with backward/forward time shifts
document.getElementsByClassName("sliderNext")[0].onclick = nextTime;
document.getElementsByClassName("sliderNext")[1].onclick = nextTime;
document.getElementsByClassName("sliderPrev")[0].onclick = prevTime;
document.getElementsByClassName("sliderPrev")[1].onclick = prevTime;
// Add key bindings, left/right arrow to move backward/forward in time
function reactKey(p_key) {
switch ( p_key ) {
// Left arrow key
case 37:
prevTime();
break;
// Right arrow key
case 39:
nextTime();
break;
}
}
window.onkeydown = function(p_event) {
reactKey(p_event.keyCode)
};
// IV. On load, add events for interface and build all figures
$(window).on("load", function() {
// Check for run ID in query string (ex. sub200331_sessInitialMRI_taskrestrun001)
let run = { name: getParameterByName("id"), index: 0, id: "1" };
if ( run.name ) {
run.id = findRunIDFromName(dataRun, run.name);
if ( run.id ) {
run.index = parseInt(run.id) - 1;
}
}
// console.log("Selecting run " + run.name + " with ID " + run.id + " and index " + run.index);
// Add initial images
let imageFolder = "assets/motion/images/";
d3.select("#motionNative").append("img")
.classed("hidden", true)
.attr("id", "spriteNative")
.attr("src", imageFolder + "target_native_" + dataRun[run.index].text + ".png");
d3.select("#motionStereo").append("img")
.classed("hidden", true)
.attr("id", "spriteStereo")
.attr("src", imageFolder + "motion_stereo_" + dataRun[run.index].text + ".png");
d3.select("#divRegistration").append("img")
.attr("id", "registration")
.attr("src", imageFolder + "target_stereo_" + dataRun[run.index].text + ".png")
.style("display", "block")
.style("margin-left", "auto")
.style("margin-right", "auto");
// $("#spriteNative").load(function() {
// selectTime(0);
// });
// Create a button to select a new session
var $eventSelect = $("#select-BOLD");
$eventSelect.select2({
placeholder: "Select a new session",
data: dataRun
});
$eventSelect.on("select2:select", function(e) {
var id = e.params.data.id;
if ( id > 0 ) {
subject = $("#select-BOLD option[value=" + id + "]").text();
// Old individual motion report HTMLs
// location.assign(["motion_report_" + subject + ".html"]);
// Dynamically load dataMotion_<runID>.js file,
// and draw charts on script load.
// vars tsl, rot, and fd are replaced in the global scope
var script = document.createElement("script");
script.onload = function(){
drawCharts(subject);
// On window resizing, trigger a re-size of all graphs
window.addEventListener("resize", function() {
selectTime(numFrame);
chartRot.m_chartRef.resize({ height: $("#registration").height() });
});
};
script.src = "assets/motion/js/dataMotion_" + subject + ".js";
document.head.appendChild(script);
// Alternate JSON data files
// runID = subject.substr(0, subject.lastIndexOf("_"));
// d3.json("assets/motion/json/dataMotion_" + subject + ".json", function(p_error, p_data) {
// runData = p_data;
// drawCharts(runID, runData);
// // On window resizing, trigger a re-size of all graphs
// window.addEventListener("resize", function() {
// selectTime(numFrame);
// chartRot.resize({ height: $("#registration").height() });
// });
// });
}
});
// Select the first run in the dropdown and trigger select event
$eventSelect.val(run.id);
$eventSelect.trigger("change");
$eventSelect.trigger({
type: "select2:select",
params: {
data: dataRun[run.index]
}
});
// Force window resize for redraw
setTimeout(function(){
$("#motionNative").hide().show(0);
$("#motionStereo").hide().show(0);
}, 1000);
});
</script>
</body>
</html>