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master
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19
.eslintrc
Normal file
19
.eslintrc
Normal file
@@ -0,0 +1,19 @@
|
||||
parserOptions:
|
||||
sourceType: module
|
||||
|
||||
extends:
|
||||
"standard"
|
||||
rules:
|
||||
no-cond-assign: 0
|
||||
no-console: 0
|
||||
semi:
|
||||
- error
|
||||
- always
|
||||
no-return-assign: 0
|
||||
one-var: 0
|
||||
env:
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es6: true
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||||
|
||||
globals:
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console: false
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performance: false
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@@ -101,8 +101,8 @@
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<br/>
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<label title="Number of iterations before the simulation is stopped">
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Iterations
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<output id="iterationsSliderOutput">300</output>
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<input type="range" min="5" max="5000" value="300" step="5" oninput="d3.select('#iterationsSliderOutput').text(value); ITERATIONS=value;">
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<output id="iterationsSliderOutput">100</output>
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<input type="range" min="5" max="1000" value="100" step="5" oninput="d3.select('#iterationsSliderOutput').text(value); ITERATIONS=value;">
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</label>
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<br/>
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||||
<label title="Attribute used for coloring nodes">
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||||
|
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@@ -2,9 +2,9 @@
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* Initialize the hybrid layout algorithm and start simulation.
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*/
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function startHybridSimulation () {
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console.log("startHybridSimulation");
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console.log('startHybridSimulation');
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springForce = false;
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||||
d3.selectAll(".nodes").remove();
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||||
d3.selectAll('.nodes').remove();
|
||||
manualStop = false;
|
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simulation.stop();
|
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p1 = performance.now();
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@@ -17,13 +17,13 @@ function startHybridSimulation() {
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.neighbourSize(NEIGHBOUR_SIZE)
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.sampleSize(SAMPLE_SIZE)
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.stableVelocity(0) // Change here
|
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.distance(distance)
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.distance(distance);
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|
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let forceFull = d3.forceNeighbourSampling()
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.neighbourSize(FULL_NEIGHBOUR_SIZE)
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.sampleSize(FULL_SAMPLE_SIZE)
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.stableVelocity(0) // Change here
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.distance(distance)
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.distance(distance);
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let hybridSimulation = d3.hybridSimulation(simulation, forceSample, forceFull)
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.sampleIterations(ITERATIONS)
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@@ -31,10 +31,10 @@ function startHybridSimulation() {
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.numPivots(PIVOTS ? NUM_PIVOTS : -1)
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.interpFindTuneIts(INTERP_ENDING_ITS)
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||||
.interpDistanceFn(distance)
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.on("sampleTick", ticked)
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.on("fullTick", ticked)
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.on("startInterp", startedFull)
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.on("end", ended);
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.on('sampleTick', ticked)
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.on('fullTick', ticked)
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||||
.on('startInterp', startedFull)
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.on('end', ended);
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let sample = hybridSimulation.subSet();
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addNodesToDOM(sample);
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||||
@@ -42,8 +42,8 @@ function startHybridSimulation() {
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hybridSimulation.restart();
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||||
function startedFull () {
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console.log("startedFull");
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||||
d3.selectAll(".nodes").remove();
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||||
console.log('startedFull');
|
||||
d3.selectAll('.nodes').remove();
|
||||
addNodesToDOM(nodes);
|
||||
}
|
||||
}
|
||||
|
||||
@@ -2,7 +2,7 @@
|
||||
* Initialize the link force algorithm and start simulation.
|
||||
*/
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||||
function startLinkSimulation () {
|
||||
console.log("startLinkSimulation")
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||||
console.log('startLinkSimulation');
|
||||
springForce = false;
|
||||
alreadyRanIterations = 0;
|
||||
manualStop = true;
|
||||
@@ -17,13 +17,12 @@ function startLinkSimulation() {
|
||||
})
|
||||
.stableVelocity(0) // Change here
|
||||
.onStableVelo(ended);
|
||||
}
|
||||
else {
|
||||
} else {
|
||||
for (i = nodes.length - 1; i >= 1; i--) {
|
||||
for (j = i - 1; j >= 0; j--) {
|
||||
links.push({
|
||||
source: nodes[i],
|
||||
target: nodes[j],
|
||||
target: nodes[j]
|
||||
});
|
||||
}
|
||||
}
|
||||
@@ -51,8 +50,8 @@ function startLinkSimulation() {
|
||||
simulation
|
||||
.alphaDecay(0)
|
||||
.alpha(1)
|
||||
.on("tick", ticked)
|
||||
.on("end", ended)
|
||||
.on('tick', ticked)
|
||||
.on('end', ended)
|
||||
// .velocityDecay(0.8)
|
||||
.force(forceName, force)
|
||||
.restart();
|
||||
|
||||
@@ -2,7 +2,7 @@
|
||||
* Initialize the Chalmers' 1996 algorithm and start simulation.
|
||||
*/
|
||||
function startNeighbourSamplingSimulation () {
|
||||
console.log("startNeighbourSamplingSimulation");
|
||||
console.log('startNeighbourSamplingSimulation');
|
||||
// springForce = true;
|
||||
alreadyRanIterations = 0;
|
||||
manualStop = true;
|
||||
@@ -21,8 +21,8 @@ function startNeighbourSamplingSimulation() {
|
||||
simulation
|
||||
.alphaDecay(0)
|
||||
.alpha(1)
|
||||
.on("tick", ticked)
|
||||
.on("end", ended)
|
||||
.on('tick', ticked)
|
||||
.on('end', ended)
|
||||
.force(forceName, force);
|
||||
// Restart the simulation.
|
||||
simulation.restart();
|
||||
|
||||
@@ -26,15 +26,15 @@ function starttSNE() {
|
||||
* Initialize the Barnes-Hut algorithm and start simulation.
|
||||
*/
|
||||
function startBarnesHutSimulation () {
|
||||
console.log("startBarnesHutSimulation")
|
||||
console.log('startBarnesHutSimulation');
|
||||
alreadyRanIterations = 0;
|
||||
manualStop = false;
|
||||
springForce = false;
|
||||
p1 = performance.now();
|
||||
|
||||
simulation.alphaDecay(1 - Math.pow(0.001, 1 / ITERATIONS))
|
||||
.on("tick", ticked)
|
||||
.on("end", ended)
|
||||
.on('tick', ticked)
|
||||
.on('end', ended)
|
||||
.force(forceName, d3.forceBarnesHut()
|
||||
// The distance function that will be used to calculate distances
|
||||
// between nodes.
|
||||
|
||||
@@ -12,7 +12,7 @@ function calculateCosineSimilarity(source, target, properties, normArgs) {
|
||||
// Iterate through every column of data
|
||||
for (var i = 0; i < properties.length; i++) {
|
||||
property = properties[i];
|
||||
if (property.toLowerCase() !== "class" && property.toLowerCase() !== "app" && property.toLowerCase() !== "user" && property.toLowerCase() !== "weekday") {
|
||||
if (property.toLowerCase() !== 'class' && property.toLowerCase() !== 'app' && property.toLowerCase() !== 'user' && property.toLowerCase() !== 'weekday') {
|
||||
var s = source[property],
|
||||
t = target[property];
|
||||
|
||||
|
||||
@@ -12,7 +12,7 @@ function calculateDiceDissimilarity(source, target, properties, normArgs) {
|
||||
// Iterate through every column of data
|
||||
for (var i = 0; i < properties.length; i++) {
|
||||
property = properties[i];
|
||||
if (property.toLowerCase() !== "class" && property.toLowerCase() !== "app" && property.toLowerCase() !== "user" && property.toLowerCase() !== "weekday") {
|
||||
if (property.toLowerCase() !== 'class' && property.toLowerCase() !== 'app' && property.toLowerCase() !== 'user' && property.toLowerCase() !== 'weekday') {
|
||||
var s = source[property],
|
||||
t = target[property];
|
||||
|
||||
|
||||
@@ -19,8 +19,8 @@ function calculateDistance(source, target, properties, normArgs) {
|
||||
// Iterate through every column of data
|
||||
for (var i = 0; i < properties.length; i++) {
|
||||
property = properties[i];
|
||||
if (source.hasOwnProperty(property) && target.hasOwnProperty(property)
|
||||
&& property.toLowerCase() !== "index" && property.toLowerCase() !== "type") {
|
||||
if (source.hasOwnProperty(property) && target.hasOwnProperty(property) &&
|
||||
property.toLowerCase() !== 'index' && property.toLowerCase() !== 'type') {
|
||||
var s = source[property],
|
||||
t = target[property];
|
||||
|
||||
@@ -42,9 +42,8 @@ function calculateDistance(source, target, properties, normArgs) {
|
||||
// Comparing Dates
|
||||
var parsedDateS = Date.parse(s);
|
||||
var parsedDateT = Date.parse(t);
|
||||
if (isNaN(s) && !isNaN(parsedDateS)
|
||||
&& isNaN(t) && !isNaN(parsedDateT)) {
|
||||
|
||||
if (isNaN(s) && !isNaN(parsedDateS) &&
|
||||
isNaN(t) && !isNaN(parsedDateT)) {
|
||||
val1 = parsedDateS.valueOf(),
|
||||
val2 = parsedDateT.valueOf();
|
||||
|
||||
|
||||
@@ -10,7 +10,7 @@ function calculateDistancePoker(source, target) {
|
||||
var sumDiff = 0.0,
|
||||
ordDiff = 1.0,
|
||||
ORD_FACTOR = 1.5,
|
||||
cards = ["C1", "C2", "C3", "C4", "C5"],
|
||||
cards = ['C1', 'C2', 'C3', 'C4', 'C5'],
|
||||
cols = 0;
|
||||
|
||||
// Iterate through cards
|
||||
@@ -26,13 +26,13 @@ function calculateDistancePoker(source, target) {
|
||||
|
||||
// Class of poker hands describes the similarities the best
|
||||
// so give it more priority than checking the differences between cards.
|
||||
if (source.hasOwnProperty("CLASS") && target.hasOwnProperty("CLASS")) {
|
||||
var s = parseInt(source["CLASS"]),
|
||||
t = parseInt(target["CLASS"]);
|
||||
if (source.hasOwnProperty('CLASS') && target.hasOwnProperty('CLASS')) {
|
||||
var s = parseInt(source['CLASS']),
|
||||
t = parseInt(target['CLASS']);
|
||||
|
||||
// If classes differ, then scale them by a factor.
|
||||
if (s !== t) {
|
||||
ordDiff *= (ORD_FACTOR * (Math.abs(s-t)))
|
||||
ordDiff *= (ORD_FACTOR * (Math.abs(s - t)));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -12,7 +12,7 @@ function calculateEuclideanDistance(source, target, properties, normArgs) {
|
||||
// Iterate through every column of data
|
||||
for (var i = 0; i < properties.length; i++) {
|
||||
property = properties[i];
|
||||
if (property.toLowerCase() !== "class" && property.toLowerCase() !== "app" && property.toLowerCase() !== "user" && property.toLowerCase() !== "weekday" && property.toLowerCase() !== "type") {
|
||||
if (property.toLowerCase() !== 'class' && property.toLowerCase() !== 'app' && property.toLowerCase() !== 'user' && property.toLowerCase() !== 'weekday' && property.toLowerCase() !== 'type') {
|
||||
var s = source[property],
|
||||
t = target[property];
|
||||
|
||||
|
||||
@@ -15,7 +15,7 @@ function calculateEuclideanDistanceTSNE(source, target, properties, normArgs) {
|
||||
for (var i = 0; i < properties.length; i++) {
|
||||
property = properties[i];
|
||||
if (source.hasOwnProperty(property) && target.hasOwnProperty(property) &&
|
||||
property.toLowerCase() !== "class") {
|
||||
property.toLowerCase() !== 'class') {
|
||||
var s = source[property],
|
||||
t = target[property];
|
||||
|
||||
|
||||
@@ -12,7 +12,7 @@ function calculateJaccardDissimilarity(source, target, properties, normArgs) {
|
||||
// Iterate through every column of data
|
||||
for (var i = 0; i < properties.length; i++) {
|
||||
property = properties[i];
|
||||
if (property.toLowerCase() !== "class" && property.toLowerCase() !== "app" && property.toLowerCase() !== "user" && property.toLowerCase() !== "weekday") {
|
||||
if (property.toLowerCase() !== 'class' && property.toLowerCase() !== 'app' && property.toLowerCase() !== 'user' && property.toLowerCase() !== 'weekday') {
|
||||
var s = source[property],
|
||||
t = target[property];
|
||||
|
||||
|
||||
@@ -13,7 +13,7 @@ function calculateManhattanDistance(source, target, properties, normArgs) {
|
||||
// Iterate through every column of data
|
||||
for (var i = 0; i < properties.length; i++) {
|
||||
property = properties[i];
|
||||
if (property.toLowerCase() !== "class" && property.toLowerCase() !== "app" && property.toLowerCase() !== "user" && property.toLowerCase() !== "weekday") {
|
||||
if (property.toLowerCase() !== 'class' && property.toLowerCase() !== 'app' && property.toLowerCase() !== 'user' && property.toLowerCase() !== 'weekday') {
|
||||
var s = source[property],
|
||||
t = target[property];
|
||||
|
||||
|
||||
@@ -23,10 +23,8 @@ function calculateNormalization(nodes) {
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
function standardDevation (nodes, properties, avg) {
|
||||
|
||||
var stDev = new Array(properties.length).fill(0)
|
||||
var stDev = new Array(properties.length).fill(0);
|
||||
|
||||
for (var i = 0; i < properties.length; i++) {
|
||||
var sum = 0;
|
||||
@@ -52,7 +50,6 @@ function standardDevation(nodes, properties, avg) {
|
||||
}
|
||||
|
||||
return stDev;
|
||||
|
||||
}
|
||||
|
||||
// Calculate the sum of values and the squared sum
|
||||
|
||||
@@ -2,22 +2,22 @@
|
||||
var width = +document.getElementById('svg').clientWidth,
|
||||
height = +document.getElementById('svg').clientHeight;
|
||||
|
||||
var svg = d3.select("svg")
|
||||
.call(d3.zoom().scaleExtent([0.0001, 1000000]).on("zoom", function () {
|
||||
svg.attr("transform", d3.event.transform);
|
||||
var svg = d3.select('svg')
|
||||
.call(d3.zoom().scaleExtent([0.0001, 1000000]).on('zoom', function () {
|
||||
svg.attr('transform', d3.event.transform);
|
||||
}))
|
||||
.append("g");
|
||||
.append('g');
|
||||
|
||||
var div = d3.select("body").append("div")
|
||||
.attr("class", "tooltip")
|
||||
.style("opacity", 0);
|
||||
var div = d3.select('body').append('div')
|
||||
.attr('class', 'tooltip')
|
||||
.style('opacity', 0);
|
||||
|
||||
var brush = d3.brush()
|
||||
.extent([[-9999999, -9999999], [9999999, 9999999]])
|
||||
.on("end", brushEnded);
|
||||
.on('end', brushEnded);
|
||||
|
||||
svg.append("g")
|
||||
.attr("class", "brush")
|
||||
svg.append('g')
|
||||
.attr('class', 'brush')
|
||||
.call(brush);
|
||||
|
||||
// var intercom = Intercom.getInstance();
|
||||
@@ -35,10 +35,10 @@ var nodes, // as in Data points
|
||||
simulation,
|
||||
velocities = [],
|
||||
rendering = true, // Rendering during the execution.
|
||||
forceName = "forces",
|
||||
forceName = 'forces',
|
||||
springForce = false,
|
||||
tooltipWidth = 0,
|
||||
fileName = "",
|
||||
fileName = '',
|
||||
selectedData,
|
||||
clickedIndex = -1,
|
||||
paused = false,
|
||||
@@ -54,10 +54,10 @@ var MULTIPLIER = 50,
|
||||
SAMPLE_SIZE = 10,
|
||||
PIVOTS = false,
|
||||
NUM_PIVOTS = 3,
|
||||
ITERATIONS = 300,
|
||||
ITERATIONS = 100,
|
||||
FULL_ITERATIONS = 20,
|
||||
NODE_SIZE = 10,
|
||||
COLOR_ATTRIBUTE = "",
|
||||
COLOR_ATTRIBUTE = '',
|
||||
FULL_NEIGHBOUR_SIZE = 10,
|
||||
FULL_SAMPLE_SIZE = 10,
|
||||
INTERP_ENDING_ITS = 20;
|
||||
@@ -68,7 +68,7 @@ var color = d3.scaleOrdinal(d3.schemeCategory10);
|
||||
$(document).ready(function () {
|
||||
distanceFunction = calculateDistance;
|
||||
d3.select('#startSimulation').on('click', startHybridSimulation);
|
||||
$("#HLParameters").show();
|
||||
$('#HLParameters').show();
|
||||
});
|
||||
|
||||
/**
|
||||
@@ -77,7 +77,7 @@ $(document).ready(function() {
|
||||
*/
|
||||
function parseFile (evt) {
|
||||
// Clear the previous nodes
|
||||
d3.selectAll(".nodes").remove();
|
||||
d3.selectAll('.nodes').remove();
|
||||
springForce = false;
|
||||
|
||||
fileName = evt.target.files[0].name;
|
||||
@@ -112,12 +112,11 @@ function processData(data, error) {
|
||||
var opts = document.getElementById('color_attr').options;
|
||||
|
||||
props.forEach(function (d) {
|
||||
opts.add(new Option(d, d, (d === COLOR_ATTRIBUTE) ? true : false));
|
||||
opts.add(new Option(d, d, (d === COLOR_ATTRIBUTE)));
|
||||
});
|
||||
opts.selectedIndex = props.length - 1;
|
||||
// props.pop(); //Hide Iris index / last column from the distance function
|
||||
|
||||
|
||||
// Put the nodes at (0,0)
|
||||
nodes.forEach(function (d) {
|
||||
d.x = 0;
|
||||
@@ -135,49 +134,48 @@ function processData(data, error) {
|
||||
};
|
||||
|
||||
function addNodesToDOM (data) {
|
||||
node = svg.append("g")
|
||||
.attr("class", "nodes")
|
||||
.selectAll("circle")
|
||||
node = svg.append('g')
|
||||
.attr('class', 'nodes')
|
||||
.selectAll('circle')
|
||||
.data(data)
|
||||
.enter().append("circle")
|
||||
.attr("r", NODE_SIZE)
|
||||
.attr("transform", "translate(" + width / 2 + "," + height / 2 + ")")
|
||||
.enter().append('circle')
|
||||
.attr('r', NODE_SIZE)
|
||||
.attr('transform', 'translate(' + width / 2 + ',' + height / 2 + ')')
|
||||
// Color code the data points by a property (for Poker Hands,
|
||||
// it is a CLASS property).
|
||||
.attr("fill", function (d) {
|
||||
.attr('fill', function (d) {
|
||||
return color(d[COLOR_ATTRIBUTE]);
|
||||
})
|
||||
.on("mouseover", function (d) {
|
||||
.on('mouseover', function (d) {
|
||||
div.transition()
|
||||
.duration(200)
|
||||
.style("opacity", .9);
|
||||
.style('opacity', 0.9);
|
||||
div.html(formatTooltip(d))
|
||||
.style("left", (d3.event.pageX) + "px")
|
||||
.style("top", (d3.event.pageY - (15 * props.length)) + "px")
|
||||
.style("width", (6 * tooltipWidth) + "px")
|
||||
.style("height", (14 * props.length) + "px");
|
||||
.style('left', (d3.event.pageX) + 'px')
|
||||
.style('top', (d3.event.pageY - (15 * props.length)) + 'px')
|
||||
.style('width', (6 * tooltipWidth) + 'px')
|
||||
.style('height', (14 * props.length) + 'px');
|
||||
highlightOnHover(d[COLOR_ATTRIBUTE]);
|
||||
})
|
||||
.on("mouseout", function (d) {
|
||||
.on('mouseout', function (d) {
|
||||
div.transition()
|
||||
.duration(500)
|
||||
.style("opacity", 0);
|
||||
node.attr("opacity", 1);
|
||||
.style('opacity', 0);
|
||||
node.attr('opacity', 1);
|
||||
})
|
||||
.on("click", function (d) {
|
||||
console.log("click", clickedIndex);
|
||||
.on('click', function (d) {
|
||||
console.log('click', clickedIndex);
|
||||
if (clickedIndex !== d.index) {
|
||||
if (springForce) {
|
||||
highlightNeighbours(Array.from(simulation.force(forceName).nodeNeighbours(d.index).keys()));
|
||||
clickedIndex = d.index;
|
||||
}
|
||||
} else {
|
||||
node.attr("r", NODE_SIZE).attr("stroke-width", 0);
|
||||
node.attr('r', NODE_SIZE).attr('stroke-width', 0);
|
||||
clickedIndex = -1;
|
||||
}
|
||||
});
|
||||
if (selectedData)
|
||||
unSelectNodes(selectedData);
|
||||
if (selectedData) { unSelectNodes(selectedData); }
|
||||
}
|
||||
|
||||
function ticked () {
|
||||
@@ -185,10 +183,10 @@ function ticked() {
|
||||
// If rendering is selected, then draw at every iteration.
|
||||
if (rendering === true) {
|
||||
node // Each sub-circle in the SVG, update cx and cy
|
||||
.attr("cx", function (d) {
|
||||
.attr('cx', function (d) {
|
||||
return d.x * MULTIPLIER;
|
||||
})
|
||||
.attr("cy", function (d) {
|
||||
.attr('cy', function (d) {
|
||||
return d.y * MULTIPLIER;
|
||||
});
|
||||
}
|
||||
@@ -196,7 +194,7 @@ function ticked() {
|
||||
// if (springForce) {
|
||||
// intercom.emit("passedData", simulation.force(forceName).distributionData());
|
||||
// }
|
||||
if(manualStop && alreadyRanIterations == ITERATIONS) {
|
||||
if (manualStop && alreadyRanIterations === ITERATIONS) {
|
||||
ended();
|
||||
}
|
||||
}
|
||||
@@ -206,10 +204,10 @@ function ended() {
|
||||
simulation.force(forceName, null);
|
||||
if (rendering !== true) { // Never drawn anything before? Now it's time.
|
||||
node
|
||||
.attr("cx", function (d) {
|
||||
.attr('cx', function (d) {
|
||||
return d.x * MULTIPLIER;
|
||||
})
|
||||
.attr("cy", function (d) {
|
||||
.attr('cy', function (d) {
|
||||
return d.y * MULTIPLIER;
|
||||
});
|
||||
}
|
||||
@@ -217,7 +215,7 @@ function ended() {
|
||||
if (p1 !== 0) {
|
||||
// Performance time measurement
|
||||
p2 = performance.now();
|
||||
console.log("Execution time: " + (p2 - p1));
|
||||
console.log('Execution time: ' + (p2 - p1));
|
||||
p1 = 0;
|
||||
p2 = 0;
|
||||
}
|
||||
@@ -228,7 +226,6 @@ function brushEnded() {
|
||||
results = [];
|
||||
|
||||
if (s) {
|
||||
|
||||
var x0 = s[0][0] - width / 2,
|
||||
y0 = s[0][1] - height / 2,
|
||||
x1 = s[1][0] - width / 2,
|
||||
@@ -247,22 +244,21 @@ function brushEnded() {
|
||||
|
||||
// intercom.emit("select", { name: fileName, indices: results });
|
||||
|
||||
d3.select(".brush").call(brush.move, null);
|
||||
d3.select('.brush').call(brush.move, null);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Format the tooltip for the data
|
||||
* @param {*} node
|
||||
*/
|
||||
function formatTooltip (node) {
|
||||
var textString = "",
|
||||
temp = "";
|
||||
var textString = '',
|
||||
temp = '';
|
||||
|
||||
tooltipWidth = 0;
|
||||
props.forEach(function (element) {
|
||||
temp = element + ": " + node[element] + "<br/>";
|
||||
temp = element + ': ' + node[element] + '<br/>';
|
||||
textString += temp;
|
||||
if (temp.length > tooltipWidth) {
|
||||
tooltipWidth = temp.length;
|
||||
@@ -287,7 +283,7 @@ function stopSimulation() {
|
||||
* @return {number} the mean of the array.
|
||||
*/
|
||||
function getAverage (array) {
|
||||
console.log("getAverage", array);
|
||||
console.log('getAverage', array);
|
||||
var total = 0;
|
||||
for (var i = 0; i < array.length; i++) {
|
||||
total += array[i];
|
||||
@@ -303,7 +299,7 @@ function unSelectNodes(data) {
|
||||
selectedData = data;
|
||||
if (fileName === data.name && nodes) {
|
||||
node
|
||||
.classed("notSelected", function (d) {
|
||||
.classed('notSelected', function (d) {
|
||||
if (data.indices.indexOf(d.index) < 0) {
|
||||
return true;
|
||||
}
|
||||
@@ -312,35 +308,33 @@ function unSelectNodes(data) {
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Highlight the neighbours for neighbour and sampling algorithm
|
||||
* @param {*} indices
|
||||
*/
|
||||
function highlightNeighbours (indices) {
|
||||
node
|
||||
.attr("r", function (d) {
|
||||
.attr('r', function (d) {
|
||||
if (indices.indexOf(d.index) >= 0) {
|
||||
return NODE_SIZE * 2;
|
||||
}
|
||||
return NODE_SIZE;
|
||||
})
|
||||
.attr("stroke-width", function (d) {
|
||||
.attr('stroke-width', function (d) {
|
||||
if (indices.indexOf(d.index) >= 0) {
|
||||
return NODE_SIZE * 0.2 + "px";
|
||||
return NODE_SIZE * 0.2 + 'px';
|
||||
}
|
||||
return "0px";
|
||||
return '0px';
|
||||
})
|
||||
.attr("stroke", "white");
|
||||
.attr('stroke', 'white');
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Highlight all the nodes with the same class on hover
|
||||
* @param {*} highlighValue
|
||||
*/
|
||||
function highlightOnHover (highlighValue) {
|
||||
node.attr("opacity", function (d) {
|
||||
node.attr('opacity', function (d) {
|
||||
return (highlighValue === d[COLOR_ATTRIBUTE]) ? 1 : 0.3;
|
||||
});
|
||||
}
|
||||
@@ -349,12 +343,11 @@ function highlightOnHover(highlighValue) {
|
||||
* Color the nodes according to given attribute.
|
||||
*/
|
||||
function colorToAttribute () {
|
||||
node.attr("fill", function (d) {
|
||||
return color(d[COLOR_ATTRIBUTE])
|
||||
node.attr('fill', function (d) {
|
||||
return color(d[COLOR_ATTRIBUTE]);
|
||||
});
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Update the distance range.
|
||||
|
||||
@@ -364,7 +357,6 @@ function updateDistanceRange() {
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Implemented pause/resume functionality
|
||||
*/
|
||||
@@ -373,17 +365,16 @@ function pauseUnPause() {
|
||||
if (paused) {
|
||||
simulation.force(forceName);
|
||||
simulation.restart();
|
||||
d3.select("#pauseButton").text("Pause");
|
||||
d3.select('#pauseButton').text('Pause');
|
||||
paused = false;
|
||||
} else {
|
||||
simulation.stop();
|
||||
d3.select("#pauseButton").text("Resume");
|
||||
d3.select('#pauseButton').text('Resume');
|
||||
paused = true;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Average distances for each node.
|
||||
* @param {*} dataNodes
|
||||
|
||||
12
index.js
12
index.js
@@ -1,17 +1,17 @@
|
||||
export {default as forceNeighbourSampling}
|
||||
from "./src/neighbourSampling";
|
||||
from './src/neighbourSampling';
|
||||
|
||||
export {default as forceBarnesHut}
|
||||
from "./src/barnesHut";
|
||||
from './src/barnesHut';
|
||||
|
||||
export {default as tSNE}
|
||||
from "./src/t-sne";
|
||||
from './src/t-sne';
|
||||
|
||||
export {default as forceLinkCompleteGraph}
|
||||
from "./src/link";
|
||||
from './src/link';
|
||||
|
||||
export {default as hybridSimulation}
|
||||
from "./src/hybridSimulation";
|
||||
from './src/hybridSimulation';
|
||||
|
||||
export {getStress as calculateStress}
|
||||
from "./src/stress";
|
||||
from './src/stress';
|
||||
|
||||
@@ -12,11 +12,19 @@
|
||||
"main": "build/d3-spring-model.js",
|
||||
"jsnext:main": "index",
|
||||
"scripts": {
|
||||
"lintcheck": "eslint index.js src",
|
||||
"lintfix": "eslint index.js src --fix",
|
||||
"build": "rm -rf build && mkdir build && rollup -g d3-force:d3,d3-dispatch:d3,d3-quadtree:d3,d3-collection:d3 -f umd -n d3 -o build/d3-spring-model.js -- index.js",
|
||||
"minify": "node_modules/uglify-es/bin/uglifyjs build/d3-spring-model.js -c -m -o build/d3-spring-model.min.js",
|
||||
"zip": "zip -j build/d3-spring-model.zip -- LICENSE README.md build/d3-spring-model.js build/d3-spring-model.min.js"
|
||||
},
|
||||
"devDependencies": {
|
||||
"eslint": "4",
|
||||
"eslint-config-standard": "^11.0.0",
|
||||
"eslint-plugin-import": "^2.9.0",
|
||||
"eslint-plugin-node": "^6.0.1",
|
||||
"eslint-plugin-promise": "^3.7.0",
|
||||
"eslint-plugin-standard": "^3.0.1",
|
||||
"rollup": "0.36",
|
||||
"uglify-js": "git+https://github.com/mishoo/UglifyJS2.git#harmony"
|
||||
},
|
||||
|
||||
@@ -1,7 +1,7 @@
|
||||
import constant from "./constant";
|
||||
import jiggle from "./jiggle";
|
||||
import {x, y} from "./xy";
|
||||
import {quadtree} from "d3-quadtree";
|
||||
import constant from './constant';
|
||||
import jiggle from './jiggle';
|
||||
import {x, y} from './xy';
|
||||
import {quadtree} from 'd3-quadtree';
|
||||
|
||||
/**
|
||||
* The refinement of the existing Barnes-Hut implementation in D3
|
||||
@@ -28,7 +28,7 @@ export default function() {
|
||||
function force (_) {
|
||||
var i, n = nodes.length, tree = quadtree(nodes, x, y).visitAfter(accumulate);
|
||||
for (alpha = _, i = 0; i < n; ++i) {
|
||||
node = nodes[i], tree.visit(apply);
|
||||
node = nodes[i]; tree.visit(apply);
|
||||
}
|
||||
}
|
||||
|
||||
@@ -52,10 +52,7 @@ export default function() {
|
||||
quad.data = children[Math.floor(Math.random() * children.length)];
|
||||
quad.x = quad.data.x;
|
||||
quad.y = quad.data.y;
|
||||
}
|
||||
|
||||
// For leaf nodes, accumulate forces from coincident quadrants.
|
||||
else {
|
||||
} else { // For leaf nodes, accumulate forces from coincident quadrants.
|
||||
q = quad;
|
||||
q.x = q.data.x;
|
||||
q.y = q.data.y;
|
||||
@@ -73,7 +70,6 @@ export default function() {
|
||||
* @return {boolean} - true if the approximation was applied.
|
||||
*/
|
||||
function apply (quad, x1, _, x2) {
|
||||
|
||||
var x = quad.data.x + quad.data.vx - node.x - node.vx,
|
||||
y = quad.data.y + quad.data.vy - node.y - node.vy,
|
||||
w = x2 - x1,
|
||||
@@ -82,35 +78,34 @@ export default function() {
|
||||
// Apply the Barnes-Hut approximation if possible.
|
||||
// Limit forces for very close nodes; randomize direction if coincident.
|
||||
if (w / l < theta) {
|
||||
if (x === 0) x = jiggle(), l += x * x;
|
||||
if (y === 0) y = jiggle(), l += y * y;
|
||||
if (x === 0) { x = jiggle(); l += x * x; }
|
||||
if (y === 0) { y = jiggle(); l += y * y; }
|
||||
if (quad.data) {
|
||||
l = (l - +distance(node, quad.data)) / l * alpha;
|
||||
x *= l, y *= l;
|
||||
x *= l; y *= l;
|
||||
quad.data.vx -= x;
|
||||
quad.data.vy -= y;
|
||||
node.vx += x;
|
||||
node.vy += y;
|
||||
}
|
||||
return true;
|
||||
}
|
||||
|
||||
// Otherwise, process points directly.
|
||||
else if (quad.length) return;
|
||||
} else if (quad.length) return; // Otherwise, process points directly.
|
||||
|
||||
// Limit forces for very close nodes; randomize direction if coincident.
|
||||
if (quad.data !== node || quad.next) {
|
||||
if (x === 0) x = jiggle(), l += x * x;
|
||||
if (y === 0) y = jiggle(), l += y * y;
|
||||
if (x === 0) { x = jiggle(); l += x * x; }
|
||||
if (y === 0) { y = jiggle(); l += y * y; }
|
||||
}
|
||||
|
||||
do if (quad.data !== node) {
|
||||
do {
|
||||
if (quad.data !== node) {
|
||||
l = (l - +distance(node, quad.data)) / l * alpha;
|
||||
x *= l, y *= l;
|
||||
x *= l; y *= l;
|
||||
quad.data.vx -= x;
|
||||
quad.data.vy -= y;
|
||||
node.vx += x;
|
||||
node.vy += y;
|
||||
}
|
||||
} while (quad = quad.next);
|
||||
}
|
||||
|
||||
@@ -125,7 +120,7 @@ export default function() {
|
||||
for (var i = 0, source, target, realDist, highDist; i < nodes.length; i++) {
|
||||
for (var j = 0; j < nodes.length; j++) {
|
||||
if (i !== j) {
|
||||
source = nodes[i], target = nodes[j];
|
||||
source = nodes[i]; target = nodes[j];
|
||||
realDist = Math.hypot(target.x - source.x, target.y - source.y);
|
||||
highDist = +distance(nodes[i], nodes[j]);
|
||||
totalDiffSq += Math.pow(realDist - highDist, 2);
|
||||
@@ -143,7 +138,7 @@ export default function() {
|
||||
};
|
||||
|
||||
force.distance = function (_) {
|
||||
return arguments.length ? (distance = typeof _ === "function" ? _ : constant(+_), force) : distance;
|
||||
return arguments.length ? (distance = typeof _ === 'function' ? _ : constant(+_), force) : distance;
|
||||
};
|
||||
|
||||
force.theta = function (_) {
|
||||
|
||||
@@ -1,8 +1,8 @@
|
||||
import {dispatch} from "d3-dispatch";
|
||||
import constant from "./constant";
|
||||
import interpBruteForce from "./interpolation/interpBruteForce";
|
||||
import interpolationPivots from "./interpolation/interpolationPivots";
|
||||
import {takeSampleFrom} from "./interpolation/helpers";
|
||||
import {dispatch} from 'd3-dispatch';
|
||||
import constant from './constant';
|
||||
import interpBruteForce from './interpolation/interpBruteForce';
|
||||
import interpolationPivots from './interpolation/interpolationPivots';
|
||||
import {takeSampleFrom} from './interpolation/helpers';
|
||||
|
||||
/**
|
||||
* An implementation of Chalmers, Morrison, and Ross' 2002 hybrid layout
|
||||
@@ -36,25 +36,25 @@ export default function (sim, forceS, forceF) {
|
||||
simulation = sim,
|
||||
forceSample = forceS,
|
||||
forceFull = forceF,
|
||||
event = d3.dispatch("sampleTick", "fullTick", "startInterp", "end"),
|
||||
event = dispatch('sampleTick', 'fullTick', 'startInterp', 'end'),
|
||||
initAlready = false,
|
||||
nodes,
|
||||
alreadyRanIterations,
|
||||
hybrid;
|
||||
|
||||
if(simulation != undefined) initSimulation();
|
||||
if(forceS != undefined || forceF != undefined) initForces();
|
||||
if (simulation !== undefined) initSimulation();
|
||||
if (forceS !== undefined || forceF !== undefined) initForces();
|
||||
|
||||
// Performed on first run
|
||||
function initialize () {
|
||||
initAlready = true;
|
||||
alreadyRanIterations = 0;
|
||||
simulation
|
||||
.on("tick", sampleTick)
|
||||
.on("end", sampleEnded)
|
||||
.on('tick', sampleTick)
|
||||
.on('end', sampleEnded)
|
||||
.nodes(sample)
|
||||
.force("Sample force", forceSample);
|
||||
console.log("Initialized Simulation for Hybrid");
|
||||
.force('Sample force', forceSample);
|
||||
console.log('Initialized Simulation for Hybrid');
|
||||
}
|
||||
|
||||
function initForces () {
|
||||
@@ -68,19 +68,20 @@ export default function (sim, forceS, forceF) {
|
||||
|
||||
// Set default value for interpDistanceFn if not been specified yet
|
||||
if (interpDistanceFn === undefined) {
|
||||
if(forceFull.distance == 'function')
|
||||
if (forceFull.distance === 'function') {
|
||||
interpDistanceFn = forceFull.distance();
|
||||
else
|
||||
} else {
|
||||
interpDistanceFn = constant(300);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
function initSimulation () {
|
||||
nodes = simulation.nodes();
|
||||
simulation
|
||||
.stop()
|
||||
.alphaDecay(0)
|
||||
.alpha(1)
|
||||
.alpha(1);
|
||||
|
||||
let sets = takeSampleFrom(nodes, Math.sqrt(nodes.length));
|
||||
sample = sets.sample;
|
||||
@@ -89,7 +90,7 @@ export default function (sim, forceS, forceF) {
|
||||
|
||||
// Sample simulation ticked 1 frame, keep track of number of iterations here.
|
||||
function sampleTick () {
|
||||
event.call("sampleTick");
|
||||
event.call('sampleTick');
|
||||
if (alreadyRanIterations++ >= SAMPLE_ITERATIONS) {
|
||||
sampleEnded();
|
||||
}
|
||||
@@ -97,7 +98,7 @@ export default function (sim, forceS, forceF) {
|
||||
|
||||
// Full simulation ticked 1 frame, keep track of number of iterations here.
|
||||
function fullTick () {
|
||||
event.call("fullTick");
|
||||
event.call('fullTick');
|
||||
if (alreadyRanIterations++ >= FULL_ITERATIONS) {
|
||||
fullEnded();
|
||||
}
|
||||
@@ -106,40 +107,40 @@ export default function (sim, forceS, forceF) {
|
||||
function fullEnded () {
|
||||
simulation.stop();
|
||||
initAlready = false;
|
||||
simulation.force("Full force", null);
|
||||
event.call("end");
|
||||
simulation.force('Full force', null);
|
||||
event.call('end');
|
||||
}
|
||||
|
||||
function sampleEnded () {
|
||||
simulation.stop();
|
||||
simulation.force("Sample force", null);
|
||||
simulation.force('Sample force', null);
|
||||
// Reset velocity of all nodes
|
||||
for (let i = sample.length - 1; i >= 0; i--) {
|
||||
sample[i].vx = 0;
|
||||
sample[i].vy = 0;
|
||||
}
|
||||
|
||||
event.call("startInterp");
|
||||
event.call('startInterp');
|
||||
if (NUM_PIVOTS >= 1) {
|
||||
interpolationPivots(sample, remainder, NUM_PIVOTS, interpDistanceFn, INTERP_FINE_ITS);
|
||||
} else {
|
||||
interpBruteForce(sample, remainder, interpDistanceFn, INTERP_FINE_ITS);
|
||||
}
|
||||
|
||||
event.call("fullTick");
|
||||
event.call('fullTick');
|
||||
alreadyRanIterations = 0;
|
||||
simulation
|
||||
.on("tick", null)
|
||||
.on("end", null) // The ending condition should be iterations count
|
||||
.on('tick', null)
|
||||
.on('end', null) // The ending condition should be iterations count
|
||||
.nodes(nodes);
|
||||
|
||||
if (FULL_ITERATIONS < 1 || forceF === undefined || forceF === null) {
|
||||
event.call("end");
|
||||
event.call('end');
|
||||
return;
|
||||
}
|
||||
simulation
|
||||
.on("tick", fullTick)
|
||||
.force("Full force", forceFull)
|
||||
.on('tick', fullTick)
|
||||
.force('Full force', forceFull)
|
||||
.restart();
|
||||
}
|
||||
|
||||
@@ -184,11 +185,11 @@ export default function (sim, forceS, forceF) {
|
||||
},
|
||||
|
||||
interpDistanceFn: function (_) {
|
||||
return arguments.length ? (interpDistanceFn = typeof _ === "function" ? _ : constant(+_), hybrid) : interpDistanceFn;
|
||||
return arguments.length ? (interpDistanceFn = typeof _ === 'function' ? _ : constant(+_), hybrid) : interpDistanceFn;
|
||||
},
|
||||
|
||||
simulation: function (_) {
|
||||
return arguments.length ? (toInit = true, simulation = _, hybrid) : simulation;
|
||||
return arguments.length ? (initAlready = false, simulation = _, hybrid) : simulation;
|
||||
},
|
||||
|
||||
forceSample: function (_) {
|
||||
@@ -197,7 +198,7 @@ export default function (sim, forceS, forceF) {
|
||||
|
||||
forceFull: function (_) {
|
||||
return arguments.length ? (forceFull = _, initForces(), hybrid) : forceFull;
|
||||
},
|
||||
}
|
||||
|
||||
};
|
||||
}
|
||||
|
||||
@@ -24,10 +24,10 @@ export function takeSampleFrom(sourceList, amount) {
|
||||
}
|
||||
|
||||
for (let i = 0; i < amount; ++i) {
|
||||
let rand = sourceList[Math.floor((Math.random() * max))];
|
||||
let rand = sourceList[Math.floor(Math.random() * max)];
|
||||
// Re-random until suitable value is found.
|
||||
while (randElements.includes(rand)) {
|
||||
rand = sourceList[Math.floor((Math.random() * max))];
|
||||
rand = sourceList[Math.floor(Math.random() * max)];
|
||||
}
|
||||
randElements.push(rand);
|
||||
}
|
||||
@@ -40,8 +40,7 @@ export function takeSampleFrom(sourceList, amount) {
|
||||
sample: remainder,
|
||||
remainder: randElements
|
||||
};
|
||||
}
|
||||
else {
|
||||
} else {
|
||||
return {
|
||||
sample: randElements,
|
||||
remainder: remainder
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
import {takeSampleFrom} from "./helpers";
|
||||
import {placeNearToNearestNeighbour} from "./interpCommon";
|
||||
import {takeSampleFrom} from './helpers';
|
||||
import {placeNearToNearestNeighbour} from './interpCommon';
|
||||
|
||||
/**
|
||||
* Perform interpolation where the "parent" node is found by brute-force.
|
||||
@@ -39,8 +39,7 @@ export default function(sampleSet, remainderSet, distanceFn, endingIts) {
|
||||
}
|
||||
|
||||
index = sampleSubset.indexOf(sample);
|
||||
if (index !== -1)
|
||||
sampleSubsetDistanceCache[index] = dist;
|
||||
if (index !== -1) { sampleSubsetDistanceCache[index] = dist; }
|
||||
}
|
||||
|
||||
placeNearToNearestNeighbour(node, nearestSample, minDist, sampleSubset, sampleSubsetDistanceCache, endingIts);
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
import {pointOnCircle, sumDistError} from "./helpers";
|
||||
import jiggle from "../jiggle";
|
||||
import {pointOnCircle, sumDistError} from './helpers';
|
||||
import jiggle from '../jiggle';
|
||||
|
||||
/**
|
||||
* Phase 2 and 3 of each node to be interpolated.
|
||||
@@ -37,16 +37,10 @@ export function placeNearToNearestNeighbour(node, nearNeighbour, radius, sampleS
|
||||
highBound = 0.0;
|
||||
|
||||
// Determine the closest quadrant
|
||||
if (dist0 == dist180) {
|
||||
if (dist90 > dist270)
|
||||
lowBound = highBound = 270;
|
||||
else
|
||||
lowBound = highBound = 90;
|
||||
} else if (dist90 == dist270) {
|
||||
if (dist0 > dist180)
|
||||
lowBound = highBound = 180;
|
||||
else
|
||||
lowBound = highBound = 0;
|
||||
if (dist0 === dist180) {
|
||||
if (dist90 > dist270) { lowBound = highBound = 270; } else { lowBound = highBound = 90; }
|
||||
} else if (dist90 === dist270) {
|
||||
if (dist0 > dist180) { lowBound = highBound = 180; } else { lowBound = highBound = 0; }
|
||||
} else if (dist0 > dist180) {
|
||||
if (dist90 > dist270) {
|
||||
lowBound = 180;
|
||||
@@ -55,15 +49,13 @@ export function placeNearToNearestNeighbour(node, nearNeighbour, radius, sampleS
|
||||
lowBound = 90;
|
||||
highBound = 180;
|
||||
}
|
||||
} else {
|
||||
if (dist90 > dist270) {
|
||||
} else if (dist90 > dist270) {
|
||||
lowBound = 270;
|
||||
highBound = 360;
|
||||
} else {
|
||||
lowBound = 0;
|
||||
highBound = 90;
|
||||
}
|
||||
}
|
||||
|
||||
// Determine the angle
|
||||
let angle = binarySearchMin(lowBound, highBound, sumDistErrorByAngle);
|
||||
@@ -95,7 +87,7 @@ function sumForcesToSample(node, samples, sampleCache) {
|
||||
y = node.y - sample.y || jiggle();
|
||||
l = Math.sqrt(x * x + y * y);
|
||||
l = (l - sampleCache[i]) / l;
|
||||
x *= l, y *= l;
|
||||
x *= l; y *= l;
|
||||
nodeVx -= x;
|
||||
nodeVy -= y;
|
||||
}
|
||||
@@ -114,7 +106,7 @@ function binarySearchMin(lb, hb, fn) {
|
||||
while (lb <= hb) {
|
||||
if (lb === hb) return lb;
|
||||
|
||||
if(hb-lb == 1) {
|
||||
if (hb - lb === 1) {
|
||||
if (fn(lb) >= fn(hb)) return hb;
|
||||
else return lb;
|
||||
}
|
||||
@@ -124,11 +116,11 @@ function binarySearchMin(lb, hb, fn) {
|
||||
valLowerHalf = fn(lb + range / 4),
|
||||
valHigherHalf = fn(lb + range * 3 / 4);
|
||||
|
||||
if (valLowerHalf > valHigherHalf)
|
||||
if (valLowerHalf > valHigherHalf) {
|
||||
lb = Math.floor((lb + hb) / 2);
|
||||
else if (valLowerHalf < valHigherHalf)
|
||||
} else if (valLowerHalf < valHigherHalf) {
|
||||
hb = Math.ceil((lb + hb) / 2);
|
||||
else {
|
||||
} else {
|
||||
lb += Math.floor(range / 4);
|
||||
hb -= Math.ceil(range / 4);
|
||||
}
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
import {takeSampleFrom} from "./helpers";
|
||||
import {placeNearToNearestNeighbour} from "./interpCommon";
|
||||
import {takeSampleFrom} from './helpers';
|
||||
import {placeNearToNearestNeighbour} from './interpCommon';
|
||||
|
||||
/**
|
||||
* Perform interpolation where the "parent" node is is estimated by pivot-based searching.
|
||||
@@ -44,8 +44,9 @@ export default function(sampleSet, remainderSet, numPivots, distanceFn, endingIt
|
||||
let distCache = []; // [ For each non-pivot sample:[For each Pivot: distance] ]
|
||||
let bucketWidths = []; // [ For each Pivot: width of each bucket ]
|
||||
|
||||
for (let i = 0; i < nonPivotSamples.length; i++)
|
||||
for (let i = 0; i < nonPivotSamples.length; i++) {
|
||||
distCache[i] = [];
|
||||
}
|
||||
|
||||
for (let j = 0; j < numPivots; j++) {
|
||||
let pivot = pivots[j];
|
||||
@@ -54,9 +55,10 @@ export default function(sampleSet, remainderSet, numPivots, distanceFn, endingIt
|
||||
for (let i = 0; i < numNonPivots; i++) {
|
||||
let sample = nonPivotSamples[i];
|
||||
distCache[i][j] = distanceFn(pivot, sample);
|
||||
if (distCache[i][j] > maxDist)
|
||||
if (distCache[i][j] > maxDist) {
|
||||
maxDist = distCache[i][j];
|
||||
}
|
||||
}
|
||||
|
||||
bucketWidths.push(maxDist / numBuckets);
|
||||
}
|
||||
@@ -77,7 +79,6 @@ export default function(sampleSet, remainderSet, numPivots, distanceFn, endingIt
|
||||
}
|
||||
// ---------------------------------------------------------------------
|
||||
|
||||
|
||||
let sampleSubset = takeSampleFrom(sampleSet, Math.sqrt(sampleSet.length)).sample;
|
||||
// Plot each of the remainder nodes
|
||||
for (let i = remainderSet.length - 1; i >= 0; i--) {
|
||||
@@ -110,12 +111,11 @@ export default function(sampleSet, remainderSet, numPivots, distanceFn, endingIt
|
||||
for (let j = pivotsBuckets[p][bucketNumber].length - 1; j >= 0; j--) {
|
||||
let candidateNode = pivotsBuckets[p][bucketNumber][j];
|
||||
let index = sampleSubset.indexOf(candidateNode);
|
||||
if (index !== -1 && sampleSubsetDistanceCache[index] !== undefined)
|
||||
dist = sampleSubsetDistanceCache[index]
|
||||
else {
|
||||
if (index !== -1 && sampleSubsetDistanceCache[index] !== undefined) {
|
||||
dist = sampleSubsetDistanceCache[index];
|
||||
} else {
|
||||
dist = distanceFn(candidateNode, node);
|
||||
if (index !== -1)
|
||||
sampleSubsetDistanceCache[index] = dist;
|
||||
if (index !== -1) { sampleSubsetDistanceCache[index] = dist; }
|
||||
}
|
||||
|
||||
if (dist < minDist) {
|
||||
@@ -127,9 +127,10 @@ export default function(sampleSet, remainderSet, numPivots, distanceFn, endingIt
|
||||
|
||||
// Fill in holes in cache
|
||||
for (let k = 0; k < sampleSubset.length; k++) {
|
||||
if (sampleSubsetDistanceCache[k] === undefined)
|
||||
if (sampleSubsetDistanceCache[k] === undefined) {
|
||||
sampleSubsetDistanceCache[k] = distanceFn(node, sampleSubset[k]);
|
||||
}
|
||||
}
|
||||
placeNearToNearestNeighbour(node, nearSample, minDist, sampleSubset, sampleSubsetDistanceCache, endingIts);
|
||||
}
|
||||
}
|
||||
|
||||
12
src/link.js
12
src/link.js
@@ -1,5 +1,5 @@
|
||||
import constant from "./constant";
|
||||
import jiggle from "./jiggle";
|
||||
import constant from './constant';
|
||||
import jiggle from './jiggle';
|
||||
|
||||
/**
|
||||
* Modified link force algorithm
|
||||
@@ -32,7 +32,8 @@ export default function() {
|
||||
// Each iteration in a tick
|
||||
for (var k = 0, source, target, i, j, x, y, l; k < iterations; ++k) {
|
||||
// For each link
|
||||
for (i = 1; i < n; i++) for (j = 0; j < i; j++) {
|
||||
for (i = 1; i < n; i++) {
|
||||
for (j = 0; j < i; j++) {
|
||||
// jiggle so l won't be zero and divide by zero error after this
|
||||
source = nodes[i];
|
||||
target = nodes[j];
|
||||
@@ -40,13 +41,14 @@ export default function() {
|
||||
y = target.y + target.vy - source.y - source.vy || jiggle();
|
||||
l = Math.sqrt(x * x + y * y);
|
||||
l = (l - distances[i * (i - 1) / 2 + j]) / l * dataSizeFactor * alpha;
|
||||
x *= l, y *= l;
|
||||
x *= l; y *= l;
|
||||
target.vx -= x;
|
||||
target.vy -= y;
|
||||
source.vx += x;
|
||||
source.vy += y;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Calculate velocity changes, aka force applied.
|
||||
if (stableVeloHandler !== null && stableVelocity >= 0) {
|
||||
@@ -90,7 +92,7 @@ export default function() {
|
||||
};
|
||||
|
||||
force.distance = function (_) {
|
||||
return arguments.length ? (distance = typeof _ === "function" ? _ : constant(+_), initializeDistance(), force) : distance;
|
||||
return arguments.length ? (distance = typeof _ === 'function' ? _ : constant(+_), initializeDistance(), force) : distance;
|
||||
};
|
||||
|
||||
force.latestAccel = function () {
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
import constant from "./constant";
|
||||
import jiggle from "./jiggle";
|
||||
import constant from './constant';
|
||||
import jiggle from './jiggle';
|
||||
/**
|
||||
* An implementation of Chalmers' 1996 Neighbour and Sampling algorithm.
|
||||
* It uses random sampling to find the most suited neighbours from the
|
||||
@@ -81,7 +81,7 @@ export default function () {
|
||||
y = target.y + target.vy - source.y - source.vy || jiggle();
|
||||
l = Math.sqrt(x * x + y * y);
|
||||
l = (l - dist) / l * dataSizeFactor * alpha;
|
||||
x *= l, y *= l;
|
||||
x *= l; y *= l;
|
||||
// Set the calculated velocites for both nodes.
|
||||
target.vx -= x;
|
||||
target.vy -= y;
|
||||
@@ -126,10 +126,10 @@ export default function () {
|
||||
break;
|
||||
}
|
||||
|
||||
let rand = Math.floor((Math.random() * max));
|
||||
let rand = Math.floor(Math.random() * max);
|
||||
// Re-random until suitable value is found.
|
||||
while (randElements.includes(rand) || exclude.includes(rand)) {
|
||||
rand = Math.floor((Math.random() * max));
|
||||
rand = Math.floor(Math.random() * max);
|
||||
}
|
||||
randElements.push(rand);
|
||||
}
|
||||
@@ -166,7 +166,6 @@ export default function () {
|
||||
return new Map(combined.slice(0, neighbourSize));
|
||||
}
|
||||
|
||||
|
||||
// API for initializing the algorithm and setting parameters
|
||||
force.initialize = function (_) {
|
||||
nodes = _;
|
||||
@@ -186,7 +185,7 @@ export default function () {
|
||||
};
|
||||
|
||||
force.distance = function (_) {
|
||||
return arguments.length ? (distance = typeof _ === "function" ? _ : constant(+_), force) : distance;
|
||||
return arguments.length ? (distance = typeof _ === 'function' ? _ : constant(+_), force) : distance;
|
||||
};
|
||||
|
||||
force.latestAccel = function () {
|
||||
|
||||
@@ -5,11 +5,12 @@
|
||||
* @return {number} - stress of the layout.
|
||||
*/
|
||||
export function getStress (nodes, distance) {
|
||||
let sumDiffSq = 0
|
||||
let sumDiffSq = 0;
|
||||
let sumLowDDistSq = 0;
|
||||
for (let j = nodes.length - 1; j >= 1; j--) {
|
||||
for (let i = 0; i < j; i++) {
|
||||
let source = nodes[i], target = nodes[j];
|
||||
let source = nodes[i];
|
||||
let target = nodes[j];
|
||||
let lowDDist = Math.hypot(target.x - source.x, target.y - source.y);
|
||||
let highDDist = distance(source, target);
|
||||
sumDiffSq += Math.pow(highDDist - lowDDist, 2);
|
||||
|
||||
18
src/t-sne.js
18
src/t-sne.js
@@ -1,4 +1,5 @@
|
||||
import constant from "./constant";
|
||||
/* eslint-disable block-scoped-var */
|
||||
import constant from './constant';
|
||||
|
||||
/**
|
||||
* Set the node id accessor to the specified i.
|
||||
@@ -52,7 +53,9 @@ export default function() {
|
||||
let u = 2 * Math.random() - 1;
|
||||
let v = 2 * Math.random() - 1;
|
||||
let r = u * u + v * v;
|
||||
if (r == 0 || r > 1) return gaussRandom();
|
||||
if (r === 0 || r > 1) {
|
||||
return gaussRandom();
|
||||
}
|
||||
return u * Math.sqrt(-2 * Math.log(r) / r);
|
||||
}
|
||||
|
||||
@@ -74,7 +77,7 @@ export default function() {
|
||||
* @return {Float64Array} - array of zeros with length n.
|
||||
*/
|
||||
function zeros (n) {
|
||||
if (typeof(n) === 'undefined' || isNaN(n)) {
|
||||
if (typeof n === 'undefined' || isNaN(n)) {
|
||||
return [];
|
||||
}
|
||||
return new Float64Array(n); // typed arrays are faster
|
||||
@@ -137,7 +140,7 @@ export default function() {
|
||||
// Normalize p and compute entropy.
|
||||
var Hhere = 0.0;
|
||||
for (j = 0; j < N; j++) {
|
||||
if (psum == 0) {
|
||||
if (psum === 0) {
|
||||
pj = 0;
|
||||
} else {
|
||||
pj = prow[j] / psum;
|
||||
@@ -158,7 +161,6 @@ export default function() {
|
||||
} else {
|
||||
beta = (beta + betamax) / 2;
|
||||
}
|
||||
|
||||
} else {
|
||||
// Converse case. Make distrubtion less peaky.
|
||||
betamax = beta;
|
||||
@@ -180,7 +182,6 @@ export default function() {
|
||||
for (j = 0; j < N; j++) {
|
||||
P1[i * N + j] = prow[j];
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
// Symmetrize P and normalize it to sum to 1 over all ij
|
||||
@@ -267,7 +268,6 @@ export default function() {
|
||||
* @return {object} that contains a cost and a gradient.
|
||||
*/
|
||||
function costGrad (Y) {
|
||||
|
||||
var pmul = iteration < 100 ? 4 : 1;
|
||||
|
||||
// Compute current Q distribution, unnormalized first.
|
||||
@@ -329,7 +329,7 @@ export default function() {
|
||||
for (var i = 0, source, target, realDist, highDist; i < nodes.length; i++) {
|
||||
for (var j = 0; j < nodes.length; j++) {
|
||||
if (i !== j) {
|
||||
source = nodes[i], target = nodes[j];
|
||||
source = nodes[i]; target = nodes[j];
|
||||
realDist = Math.hypot(target.x - source.x, target.y - source.y);
|
||||
highDist = +distance(nodes[i], nodes[j]);
|
||||
totalDiffSq += Math.pow(realDist - highDist, 2);
|
||||
@@ -355,7 +355,7 @@ export default function() {
|
||||
};
|
||||
|
||||
force.distance = function (_) {
|
||||
return arguments.length ? (distance = typeof _ === "function" ? _ : constant(+_), force) : distance;
|
||||
return arguments.length ? (distance = typeof _ === 'function' ? _ : constant(+_), force) : distance;
|
||||
};
|
||||
|
||||
force.stress = function () {
|
||||
|
||||
Reference in New Issue
Block a user