Remove unused files

This commit is contained in:
Pitchaya Boonsarngsuk
2018-02-02 10:30:19 +00:00
parent 75b0d4cdc7
commit f9c2af81b6
5 changed files with 0 additions and 1426 deletions

View File

@@ -1,195 +0,0 @@
function doInterpolation(sampleSet, remainderSet, interpSubset, properties) {
var distance = calculateDistancePoker;
// var distance = calculateEuclideanDistance;
console.log("Brute-force");
for (var i = 0; i < remainderSet.length; i++) {
var node = remainderSet[i],
minNode = sampleSet[0],
minDist = 0,
sampleCache = [];
minDist = distance(node, minNode, properties);
for (var j = 1, sample; j < sampleSet.length; j++) {
sample = sampleSet[j];
if ((sample !== node) && (distance(node, sample, properties) < minDist)) {
minDist = distance(node, sample, properties);
minNode = sample;
}
}
// console.log()
for (var k = 0; k < interpSubset.length; k++) {
sampleCache[k] = distance(node, interpSubset[k], properties);
}
var radius = distance(node, minNode, properties);
placeNearToNearestNeighbour(node, minNode, interpSubset, sampleCache, radius);
}
}
function placeNearToNearestNeighbour(node, minNode, sample, sampleCache, radius) {
var
dist0 = 0.0,
dist90 = 0.0,
dist180 = 0.0,
dist270 = 0.0,
lowBound = 0.0,
highBound = 0.0;
dist0 = sumDistToSample(node, centerPoint(0, radius, minNode.x, minNode.y), sample, sampleCache);
dist90 = sumDistToSample(node, centerPoint(90, radius, minNode.x, minNode.y), sample, sampleCache);
dist180 = sumDistToSample(node, centerPoint(180, radius, minNode.x, minNode.y), sample, sampleCache);
dist270 = sumDistToSample(node, centerPoint(270, radius, minNode.x, minNode.y), sample, sampleCache);
// console.log(dist0, dist90, dist180, dist270);
// 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;
} else if (dist0 > dist180) {
if (dist90 > dist270) {
lowBound = 180;
highBound = 270;
} else {
lowBound = 90;
highBound = 180;
}
} else {
if (dist90 > dist270) {
lowBound = 270;
highBound = 360;
} else {
lowBound = 0;
highBound = 90;
}
}
var angle = binarySearch(lowBound, highBound, minNode.x, minNode.y, radius, node, sample, sampleCache);
var newPoint = centerPoint(angle, radius, minNode.x, minNode.y);
// console.log(newPoint);
node.x = newPoint.x;
node.y = newPoint.y;
// for (var i = 0; i < 20; i++) {
// var forces = sumForcesToSample(node, sample, sampleCache);
// // console.log(forces);
// node.x += forces.x;
// node.y += forces.y;
// }
}
function centerPoint(angle, radius, posX, posY) {
var x = posX + Math.cos(toRadians(angle) * radius);
var y = posY + Math.sin(toRadians(angle) * radius);
return {
x: x,
y: y
};
}
function toRadians(degrees) {
return degrees * (Math.PI / 180);
}
function sumDistToSample(node, point, sample, sampleCache) {
var total = 0.0;
// console.log(total, sample);
for (var i = 0; i < sample.length; i++) {
var s = sample[i];
var realDist = Math.hypot(s.x - point.x, s.y - point.y);
var desDist = sampleCache[i];
total += Math.abs(realDist - desDist);
}
return total;
}
function sumForcesToSample(node, sample, sampleCache) {
var x = 0,
y = 0,
// len = 0,
dist = 0,
force,
SPRING_FORCE = 0.7;
for (var i = 0, unitX, unitY; i < sample.length; i++) {
var s = sample[i];
if (s !== node) {
unitX = s.x - node.x;
unitY = s.y - node.y;
// Normalize coordinates
len = Math.sqrt(unitX * unitX + unitY * unitY);
unitX /= len;
unitY /= len;
console.log(unitX, unitY);
var realDist = Math.sqrt(unitX * unitX + unitY * unitY);
var desDist = sampleCache[i];
dist += realDist - desDist;
force = (SPRING_FORCE * dist);
x += unitX * force;
y += unitY * force;
}
x *= (1.0 / sample.length);
y *= (1.0 / sample.length);
return {
x: x,
y: y
};
}
}
function binarySearch(lb, hb, x, y, r, node, sample, sampleCache) {
while (lb <= hb) {
var mid = Math.round((lb + hb) / 2);
if ((mid === lb) || (mid === hb)) {
if (sumDistToSample(node, centerPoint(lb, r, x, y), sample, sampleCache) >=
sumDistToSample(node, centerPoint(hb, r, x, y), sample, sampleCache)) {
return hb;
} else {
return lb;
}
} else {
var distMidLeft = sumDistToSample(node, centerPoint(mid + 1, r, x, y), sample, sampleCache);
var distMidRight = sumDistToSample(node, centerPoint(mid - 1, r, x, y), sample, sampleCache);
var distMid = sumDistToSample(node, centerPoint(mid, r, x, y), sample, sampleCache);
if (distMid > distMidLeft) {
lb = mid + 1;
} else if (distMid > distMidRight) {
hb = mid - 1;
} else {
return mid;
}
}
}
return -1;
}

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@@ -1,269 +0,0 @@
function doInterpolationPivots(sampleSet, remainderSet, interpSubset, properties) {
var distance = calculateDistancePoker;
// var distance = calculateEuclideanDistance;
// Pivot based parent finding
var numBuckets = Math.floor(Math.sqrt(sampleSet.length)),
// numPivots = Math.floor(Math.sqrt(sampleSet.length)),
numPivots = 3,
parents = [],
maxDists = [],
bucketWidths = [],
pivotsBuckets = [];
console.log("Parents, pivots=", numPivots);
var pivots = createRandomSample(sampleSet.concat(remainderSet), sampleSet.length, numPivots);
for (var i = 0; i < numPivots; i++) {
pivotsBuckets[i] = [];
for (var j = 0; j < numBuckets; j++) {
pivotsBuckets[i][j] = [];
}
}
// Pre-processing
var fullDists = []
for (var i = 0; i < sampleSet.length; i++) {
fullDists[i] = [];
}
for (var j = 0, maxDist = -1; j < numPivots; j++) {
var c1 = pivots[j];
for (var i = 0; i < sampleSet.length; i++) {
var c2 = sampleSet[i];
if (c1 !== c2) {
var dist = distance(c1, c2, properties);
// console.log(dist, c1, c2);
if (dist > maxDist) {
maxDist = dist;
}
fullDists[i][j] = dist;
} else {
fullDists[i][j] = 0.0001;
}
}
maxDists.push(maxDist);
bucketWidths.push(maxDist / numBuckets);
}
// console.log(fullDists);
for (var j = 0; j < numPivots; j++) {
var bucketWidth = bucketWidths[j];
for (var i = 0; i < sampleSet.length; i++) {
var tmp = pivotsBuckets[j][Math.floor((fullDists[i][j] - 0.0001) / bucketWidth)];
// pivotsBuckets[j][Math.floor((fullDists[i][j] - 0.0001) / bucketWidth)].push(sampleSet[i]);
// console.log(tmp, i, j, bucketWidth, Math.floor((fullDists[i][j] - 0.0001) / bucketWidth));
tmp.push(sampleSet[i]);
}
}
for (var i = 0; i < remainderSet.length; i++) {
var node = remainderSet[i],
minNode = sampleSet[0],
minDist = 0,
sampleCache = [];
// Pivot based parent search
var node = remainderSet[i];
var clDist = Number.MAX_VALUE;
for (var p = 0; p < numPivots; p++) {
var comp = pivots[p];
var bucketWidth = bucketWidths[p];
if (node !== comp) {
var dist = distance(node, comp, properties);
bNum = Math.floor((dist - 0.0001) / bucketWidth);
if (bNum >= numBuckets) {
bNum = numBuckets - 1;
} else if (bNum < 0) {
bNum = 0;
}
var bucketContents = pivotsBuckets[p][bNum];
for (var w = 0; w < bucketContents.length; w++) {
var c1 = bucketContents[w];
if (c1 != node) {
dist = distance(c1, node, properties);
if (dist <= clDist) {
clDist = dist;
minNode = bucketContents[w];
}
}
}
}
}
for (var k = 0; k < interpSubset.length; k++) {
sampleCache[k] = distance(node, interpSubset[k], properties);
}
var radius = distance(node, minNode, properties);
placeNearToNearestNeighbour(node, minNode, interpSubset, sampleCache, radius);
}
}
function placeNearToNearestNeighbour(node, minNode, sample, sampleCache, radius) {
var
dist0 = 0.0,
dist90 = 0.0,
dist180 = 0.0,
dist270 = 0.0,
lowBound = 0.0,
highBound = 0.0;
dist0 = sumDistToSample(node, centerPoint(0, radius, minNode.x, minNode.y), sample, sampleCache);
dist90 = sumDistToSample(node, centerPoint(90, radius, minNode.x, minNode.y), sample, sampleCache);
dist180 = sumDistToSample(node, centerPoint(180, radius, minNode.x, minNode.y), sample, sampleCache);
dist270 = sumDistToSample(node, centerPoint(270, radius, minNode.x, minNode.y), sample, sampleCache);
// console.log(dist0, dist90, dist180, dist270);
// 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;
} else if (dist0 > dist180) {
if (dist90 > dist270) {
lowBound = 180;
highBound = 270;
} else {
lowBound = 90;
highBound = 180;
}
} else {
if (dist90 > dist270) {
lowBound = 270;
highBound = 360;
} else {
lowBound = 0;
highBound = 90;
}
}
var angle = binarySearch(lowBound, highBound, minNode.x, minNode.y, radius, node, sample, sampleCache);
var newPoint = centerPoint(angle, radius, minNode.x, minNode.y);
// console.log(newPoint);
node.x = newPoint.x;
node.y = newPoint.y;
// for (var i = 0; i < 20; i++) {
// var forces = sumForcesToSample(node, sample, sampleCache);
// // console.log(forces);
// node.x += forces.x;
// node.y += forces.y;
// }
}
function centerPoint(angle, radius, posX, posY) {
var x = posX + Math.cos(toRadians(angle) * radius);
var y = posY + Math.sin(toRadians(angle) * radius);
return {
x: x,
y: y
};
}
function toRadians(degrees) {
return degrees * (Math.PI / 180);
}
function sumDistToSample(node, point, sample, sampleCache) {
var total = 0.0;
// console.log(total, sample);
for (var i = 0; i < sample.length; i++) {
var s = sample[i];
var realDist = Math.hypot(s.x - point.x, s.y - point.y);
var desDist = sampleCache[i];
total += Math.abs(realDist - desDist);
}
return total;
}
function sumForcesToSample(node, sample, sampleCache) {
var x = 0,
y = 0,
// len = 0,
dist = 0,
force,
SPRING_FORCE = 0.7;
for (var i = 0, unitX, unitY; i < sample.length; i++) {
var s = sample[i];
if (s !== node) {
unitX = s.x - node.x;
unitY = s.y - node.y;
// Normalize coordinates
len = Math.sqrt(unitX * unitX + unitY * unitY);
unitX /= len;
unitY /= len;
console.log(unitX, unitY);
var realDist = Math.sqrt(unitX * unitX + unitY * unitY);
var desDist = sampleCache[i];
dist += realDist - desDist;
force = (SPRING_FORCE * dist);
x += unitX * force;
y += unitY * force;
}
x *= (1.0 / sample.length);
y *= (1.0 / sample.length);
return {
x: x,
y: y
};
}
}
function binarySearch(lb, hb, x, y, r, node, sample, sampleCache) {
while (lb <= hb) {
var mid = Math.round((lb + hb) / 2);
if ((mid === lb) || (mid === hb)) {
if (sumDistToSample(node, centerPoint(lb, r, x, y), sample, sampleCache) >=
sumDistToSample(node, centerPoint(hb, r, x, y), sample, sampleCache)) {
return hb;
} else {
return lb;
}
} else {
var distMidLeft = sumDistToSample(node, centerPoint(mid + 1, r, x, y), sample, sampleCache);
var distMidRight = sumDistToSample(node, centerPoint(mid - 1, r, x, y), sample, sampleCache);
var distMid = sumDistToSample(node, centerPoint(mid, r, x, y), sample, sampleCache);
if (distMid > distMidLeft) {
lb = mid + 1;
} else if (distMid > distMidRight) {
hb = mid - 1;
} else {
return mid;
}
}
}
return -1;
}

View File

@@ -1,579 +0,0 @@
// Get the width and heigh of the SVG element.
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);
}))
.append("g");
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);
svg.append("g")
.attr("class", "brush")
.call(brush);
var intercom = Intercom.getInstance();
intercom.on("select", unSelectNodes);
var imgs = svg.selectAll("image");
var links = [],
nodes,
node,
props,
norm,
p1 = 0,
p2 = 0,
size,
distanceFunction,
simulation,
velocities = [],
rendering = true, // Rendering during the execution.
forceName = "forces",
springForce = false,
tooltipWidth = 0,
fileName = "",
selectedData,
clickedIndex = -1;
// Default parameters
var MULTIPLIER = 50,
PERPLEXITY = 30,
LEARNING_RATE = 10,
NEIGHBOUR_SIZE = 6,
SAMPLE_SIZE = 3,
PIVOTS = false,
NUM_PIVOTS = 3,
ITERATIONS = 300,
FULL_ITERATIONS = 20,
NODE_SIZE = 10,
COLOR_ATTRIBUTE = "";
// Create a color scheme for a range of numbers.
var color = d3.scaleOrdinal(d3.schemeCategory10);
/**
* Parse the data from the provided csv file using Papa Parse library
* @param {file} evt - csv file.
*/
function parseFile(evt) {
// Clear the previous nodes
d3.selectAll(".nodes").remove();
springForce = false;
fileName = evt.target.files[0].name;
Papa.parse(evt.target.files[0], {
header: true,
dynamicTyping: true,
skipEmptyLines: true,
complete: function (results) {
processData(results.data, results.error);
}
});
}
/**
* Process the data and pass it into D3 force simulation.
* @param {array} data
* @param {object} error
*/
function processData(data, error) {
if (error) throw error.message;
nodes = data;
// Number of iterations before stopping.
size = nodes.length;
console.log("Number of iterations: ", ITERATIONS);
// Start by placing the nodes at the center (its starting positions).
simulation = d3.forceSimulation();
console.log("n =", nodes.length);
// Calculate normalization arguments and get the list of
// properties of the nodes.
norm = calculateNormalization(nodes);
props = Object.keys(nodes[0]);
COLOR_ATTRIBUTE = props[0];
var opts = document.getElementById('color_attr').options;
props.forEach(function (d) {
opts.add(new Option(d, d, (d === COLOR_ATTRIBUTE) ? true : false));
});
// Add the nodes to DOM.
node = svg.append("g")
.attr("class", "nodes")
.selectAll("circle")
.data(nodes)
.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) {
return color(d[COLOR_ATTRIBUTE]);
})
.on("mouseover", function (d) {
highlightOnHover(d[COLOR_ATTRIBUTE]);
})
.on("mouseout", function (d) {
div.transition()
.duration(500)
.style("opacity", 0);
node.attr("opacity", 1);
})
.on("click", function (d) {
if (clickedIndex !== d.index) {
highlightNeighbours(d.index, springForce ? Array.from(simulation.force(forceName).nodeNeighbours(d.index).keys()) : []);
clickedIndex = d.index;
} else {
svg.selectAll("image").remove();
node.attr("r", NODE_SIZE).attr("stroke-width", 0);
clickedIndex = -1;
}
});
// Pass the nodes to the D3 force simulation.
simulation
.nodes(nodes)
.on("tick", ticked)
.on("end", ended);
function ticked() {
// If rendering is selected, then draw at every iteration.
if (rendering === true) {
node
.attr("cx", function (d) {
return d.x;
})
.attr("cy", function (d) {
return d.y;
});
}
}
function ended() {
if (rendering !== true) {
node
.attr("cx", function (d) {
return d.x;
})
.attr("cy", function (d) {
return d.y;
});
}
if (p1 !== 0) {
// Performance time measurement
p2 = performance.now();
console.log("Execution time: " + (p2 - p1));
// Do not calculate stress for data sets bigger than 100 000.
// if (nodes.length <= 100000) {
// console.log("Stress: ", simulation.force(forceName).stress());
// }
p1 = 0;
p2 = 0;
}
}
};
function brushEnded() {
var s = d3.event.selection,
results = [];
if (s) {
var x0 = s[0][0] - width / 2,
y0 = s[0][1] - height / 2,
x1 = s[1][0] - width / 2,
y1 = s[1][1] - height / 2;
if (nodes) {
var sel = node.filter(function (d) {
if (d.x > x0 && d.x < x1 && d.y > y0 && d.y < y1) {
return true;
}
return false;
}).data();
results = sel.map(function (a) { return a.index; });
}
intercom.emit("select", { name: fileName, indices: results });
d3.select(".brush").call(brush.move, null);
}
}
/**
* Initialize the Chalmers' 1996 algorithm and start simulation.
*/
function startNeighbourSamplingSimulation() {
springForce = true;
simulation.stop();
p1 = performance.now();
simulation
.alphaDecay(1 - Math.pow(0.001, 1 / ITERATIONS))
.force(forceName, d3.forceNeighbourSamplingDistance()
// Set the parameters for the algorithm (optional).
.neighbourSize(NEIGHBOUR_SIZE)
.sampleSize(SAMPLE_SIZE)
.multiplier(MULTIPLIER)
// The distance function that will be used to calculate distances
// between nodes.
.distance(function (s, t) {
return distanceFunction(s, t, props, norm);
}));
// Restart the simulation.
console.log(simulation.force(forceName).neighbourSize(), simulation.force(forceName).sampleSize());
simulation.alpha(1).restart();
}
/**
* Initialize the hybrid layout algorithm and start simulation.
*/
function startHybridSimulation() {
springForce = false;
d3.selectAll(".nodes").remove();
simulation.stop();
p1 = performance.now();
hybridSimulation = d3.hybridSimulation(nodes);
hybridSimulation
.multiplier(MULTIPLIER)
.sampleIterations(ITERATIONS)
.pivots(PIVOTS)
.numPivots(NUM_PIVOTS)
.fullIterations(FULL_ITERATIONS)
.neighbourSize(NEIGHBOUR_SIZE)
.sampleSize(SAMPLE_SIZE);
var sample = hybridSimulation.sample();
var remainder = hybridSimulation.remainder();
// Add the nodes to DOM.
node = svg.append("g")
.attr("class", "nodes")
.selectAll("circle")
.data(sample)
.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) {
return color(d[COLOR_ATTRIBUTE])
})
.on("mouseover", function (d) {
div.transition()
.duration(200)
.style("opacity", .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");
highlightOnHover(d[COLOR_ATTRIBUTE]);
})
.on("mouseout", function (d) {
div.transition()
.duration(500)
.style("opacity", 0);
node.attr("opacity", 1);
});
if (selectedData) {
unSelectNodes(selectedData);
}
hybridSimulation
.distance(distanceFunction);
hybridSimulation
.on("sampleTick", tickedHybrid)
.on("fullTick", tickedHybrid)
.on("startFull", started)
.on("end", endedHybrid);
function tickedHybrid() {
if (rendering === true) {
node
.attr("cx", function (d) {
return d.x;
})
.attr("cy", function (d) {
return d.y;
});
}
}
function started() {
d3.selectAll(".nodes").remove();
// Add the nodes to DOM.
node = svg.append("g")
.attr("class", "nodes")
.selectAll("circle")
.data(nodes)
.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) {
return color(d[COLOR_ATTRIBUTE])
})
.on("mouseover", function (d) {
div.transition()
.duration(200)
.style("opacity", .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");
highlightOnHover(d[COLOR_ATTRIBUTE]);
})
.on("mouseout", function (d) {
div.transition()
.duration(500)
.style("opacity", 0);
node.attr("opacity", 1);
});
if (selectedData) {
unSelectNodes(selectedData);
}
}
function endedHybrid() {
if (rendering !== true) {
node
.attr("cx", function (d) {
return d.x;
})
.attr("cy", function (d) {
return d.y;
});
}
// Performance time measurement
p2 = performance.now();
console.log("Execution time: " + (p2 - p1));
// Do not calculate stress for data sets bigger than 100 000.
// if (nodes.length <= 100000) {
// console.log("Stress: ", hybridSimulation.stress());
// }
p1 = 0;
p2 = 0;
}
}
/**
* Initialize the t-SNE algorithm and start simulation.
*/
function starttSNE() {
springForce = false;
simulation.stop();
p1 = performance.now();
simulation
.alphaDecay(1 - Math.pow(0.001, 1 / ITERATIONS))
.force(forceName, d3.tSNE()
// Set the parameter for the algorithm (optional).
.perplexity(PERPLEXITY)
.learningRate(LEARNING_RATE)
// The distance function that will be used to calculate distances
// between nodes.
.distance(function (s, t) {
return distanceFunction(s, t, props, norm) * MULTIPLIER;
}));
// Restart the simulation.
console.log(simulation.force(forceName).perplexity(), simulation.force(forceName).learningRate());
simulation.alpha(1).restart();
}
/**
* Initialize the Barnes-Hut algorithm and start simulation.
*/
function startBarnesHutSimulation() {
springForce = false;
simulation.stop();
p1 = performance.now();
simulation
.alphaDecay(1 - Math.pow(0.001, 1 / ITERATIONS))
.force(forceName, d3.forceBarnesHut()
// The distance function that will be used to calculate distances
// between nodes.
.distance(function (s, t) {
return distanceFunction(s, t, props, norm) * MULTIPLIER;
}));
// Restart the simulation.
simulation.alpha(1).restart();
}
/**
* Initialize the link force algorithm and start simulation.
*/
function startLinkSimulation() {
springForce = false;
simulation.stop();
p1 = performance.now();
// Initialize link array.
nodes = simulation.nodes();
for (i = 0; i < nodes.length; i++) {
for (j = 0; j < nodes.length; j++) {
if (i !== j) {
links.push({
source: nodes[i],
target: nodes[j],
});
}
}
}
// Add the links to the simulation.
simulation.force(forceName, d3.forceLink().links(links));
simulation
.alphaDecay(1 - Math.pow(0.001, 1 / ITERATIONS))
.force(forceName)
// The distance function that will be used to calculate distances
// between nodes.
.distance(function (n) {
return distanceFunction(n.source, n.target, props, norm) * MULTIPLIER;
})
// Set the parameter for the algorithm (optional).
.strength(1);
// Restart the simulation.
simulation.alpha(1).restart();
}
/**
* Halt the execution.
*/
function stopSimulation() {
simulation.stop();
if (typeof hybridSimulation !== 'undefined') {
hybridSimulation.stop();
}
}
/**
* Calculate the average values of the array.
* @param {array} array
* @return {number} the mean of the array.
*/
function getAverage(array) {
var total = 0;
for (var i = 0; i < array.length; i++) {
total += array[i];
}
return total / array.length;
}
/**
* Deselect the nodes to match the selection from other window.
* @param {*} data
*/
function unSelectNodes(data) {
selectedData = data;
if (fileName === data.name && nodes) {
node
.classed("notSelected", function (d) {
if (data.indices.indexOf(d.index) < 0) {
return true;
}
return false;
});
}
}
/**
* Highlight the neighbours for neighbour and sampling algorithm and show the corresponding MNIST images for each node.
* @param {*} indices
*/
function highlightNeighbours(index, indices) {
var selectedNodes = [nodes[index]];
indices.forEach(function (i) {
selectedNodes.push(nodes[i]);
});
var ratio = NODE_SIZE / 10;
svg.selectAll("image").remove();
imgs.data(selectedNodes).enter()
.append("svg:image")
.attr("transform", "translate(" + width / 2 + "," + height / 2 + ")")
.attr("xlink:href", function (d) {
return "data/mnist/images/" + d.index + ".png";
})
.attr("x", function (d) {
return d.x + (ratio * 20);
})
.attr("y", function (d) {
return d.y - (ratio * 20);
})
.attr("width", ratio * 28)
.attr("height", ratio * 28);
node
.attr("r", function (d) {
if (indices.indexOf(d.index) >= 0) {
return NODE_SIZE * 2;
}
return NODE_SIZE;
})
.attr("stroke-width", function (d) {
if (indices.indexOf(d.index) >= 0) {
return NODE_SIZE * 0.2 + "px";
}
return "0px";
})
.attr("stroke", "white");
}
/**
* Highlight all the nodes with the same class on hover
* @param {*} highlighValue
*/
function highlightOnHover(highlighValue) {
node.attr("opacity", function (d) {
return (highlighValue === d[COLOR_ATTRIBUTE]) ? 1 : 0.3;
});
}
/**
* Color the nodes according to given attribute.
*/
function colorToAttribute() {
node.attr("fill", function (d) {
return color(d[COLOR_ATTRIBUTE])
});
}

View File

@@ -1,109 +0,0 @@
function findPivots(dataSet, sampleSet, remainderSet) {
var distance = calculateDistancePoker;
// Initialize
var numBuckets = Math.floor(Math.sqrt(sampleSet.length)),
numPivots = Math.floor(Math.sqrt(sampleSet.length)),
parents = [],
maxDists = [],
bucketWidths = [],
pivotsBuckets = [];
var pivots = createRandomSample(dataSet, sampleSet.length, numPivots);
for (var i = 0; i < numPivots; i++) {
pivotsBuckets[i] = [];
for (var j = 0; j < numBuckets; j++) {
pivotsBuckets[i][j] = [];
}
}
// Pre-processing
var fullDists = []
for (var i = 0; i < sampleSet.length; i++) {
fullDists[i] = [];
}
for (var j = 0, maxDist = -1; j < numPivots; j++) {
var c1 = pivots[j];
for (var i = 0; i < sampleSet.length; i++) {
var c2 = sampleSet[i];
if (c1 !== c2) {
var dist = distance(c1, c2);
// console.log(dist, c1, c2);
if (dist > maxDist) {
maxDist = dist;
}
fullDists[i][j] = dist;
} else {
fullDists[i][j] = 0.0001;
}
}
maxDists.push(maxDist);
bucketWidths.push(maxDist / numBuckets);
}
// console.log(fullDists);
for (var j = 0; j < numPivots; j++) {
var bucketWidth = bucketWidths[j];
for (var i = 0; i < sampleSet.length; i++) {
var tmp = pivotsBuckets[j][Math.floor((fullDists[i][j] - 0.0001) / bucketWidth)];
// pivotsBuckets[j][Math.floor((fullDists[i][j] - 0.0001) / bucketWidth)].push(sampleSet[i]);
// console.log(tmp, i, j, bucketWidth, Math.floor((fullDists[i][j] - 0.0001) / bucketWidth));
tmp.push(sampleSet[i]);
}
}
// Find parents
for (var r = 0, bNum, minIndex; r < remainderSet.length; r++) {
var node = remainderSet[r];
var clDist = Number.MAX_VALUE;
for (var p = 0; p < numPivots; p++) {
var comp = pivots[p];
var bucketWidth = bucketWidths[p];
if (node !== comp) {
var dist = distance(node, comp);
bNum = Math.floor((dist - 0.0001) / bucketWidth);
if (bNum >= numBuckets) {
bNum = numBuckets - 1;
} else if (bNum < 0) {
bNum = 0;
}
var bucketContents = pivotsBuckets[p][bNum];
for (var w = 0; w < bucketContents.length; w++) {
var c1 = bucketContents[w];
if (c1 != node) {
dist = distance(c1, node);
if (dist <= clDist) {
clDist = dist;
minIndex = bucketContents[w];
}
}
}
}
}
parents.push(minIndex);
}
return parents;
}
function createRandomSample(nodes, max, size) {
var randElements = [];
for (var i = 0; i < size; ++i) {
// Stop when no new elements can be found.
if (randElements.size >= nodes.length) {
break;
}
var rand = Math.floor((Math.random() * max));
// If the rand is already in random list or in exclude list
// ignore it and get a new value.
while (randElements.includes(rand)) {
rand = Math.floor((Math.random() * max));
}
randElements.push(nodes[rand]);
}
return randElements;
}

View File

@@ -1,274 +0,0 @@
<!DOCTYPE html>
<html>
<meta charset="utf-8">
<style>
h1 {
text-align: center;
margin: 10px 0 10px 0;
}
.links line {
stroke: #999;
stroke-opacity: 0.6;
}
/*.nodes circle {
stroke: #fff;
stroke-width: 1.5px;
}*/
circle:hover {
fill: #8B0000;
opacity: 0.8;
}
.notSelected {
fill: #999;
opacity: 0.8;
}
.highlighted {
fill: black;
}
#svg {
border-style: solid;
margin: auto;
}
.left {
float: left;
width: 32%;
}
.controls {
flex-basis: 200px;
padding: 0 5px;
}
.controls input[type="range"] {
margin: 0 5% 0.5em 5%;
width: 90%;
}
.multiplier {
margin: 10px 0 10px 0;
}
.parameters {
margin: 10px 0 10px 30px;
}
.checkbox {
margin: 10px 0 10px 0;
}
.start {
text-align: center;
}
div.tooltip {
position: absolute;
border: 0px;
border-radius: 8px;
pointer-events: none;
}
</style>
<body>
<h1>Evaluation</h1>
<svg id="svg" width="100%" height="600">
<div class="left controls">
<div class="input">
<input type="file" id="csv-file" name="files">
</div>
<div class="multiplier">
<label title="The size of the nodes">
Node size
<output id="nodeSizeSliderOutput">10</output>
<input type="range" min="5" max="200" value="10" step="5" oninput="d3.select('#nodeSizeSliderOutput').text(value); NODE_SIZE=value; d3.selectAll('circle').attr('r', value);">
</label>
<br/>
<label title="The number that distance is multiplied by in order to improve the visibility of the graph">
distanceMultiplier
<output id="distanceMultiplierSliderOutput">50</output>
<input type="range" min="5" max="1000" value="50" step="5" oninput="d3.select('#distanceMultiplierSliderOutput').text(value); MULTIPLIER=value;">
</label>
<br/>
<label title="Number of iterations before the simulation is stopped">
Iterations
<output id="iterationsSliderOutput">300</output>
<input type="range" min="5" max="5000" value="300" step="5" oninput="d3.select('#iterationsSliderOutput').text(value); ITERATIONS=value;">
</label>
<br/>
<label title="Attribute used for coloring nodes">
Color attribute
<select id="color_attr" onchange="COLOR_ATTRIBUTE=value; colorToAttribute();">
</select>
</label>
</div>
<div class="checkbox">
<label title="js/">
Rendering
<input type="checkbox" checked onclick="rendering=!rendering;">
</label>
</div>
<div class="start">
<button id="startSimulation" form="algorithmForm">Start</button>
<button onclick="stopSimulation()">Stop</button>
</div>
</div>
<div class="left">
<p>Select algorithm:</p>
<div id="algorithms">
<input id="HLButton" type="radio" name="algorithm" onclick="d3.select('#startSimulation').on('click', startHybridSimulation)">Hybrid
layout
<br>
<div id="HLParameters" class="parameters" style="display:none">
<div id="pivots">
<input id="BFButton" type="radio" name="pivots" checked="checked" onclick="PIVOTS=false;">Brute-force<br>
<input id="PButton" type="radio" name="pivots" onclick="PIVOTS=true;">Pivots<br>
<div id="numPivots" class="parameters" style="display:none">
<label title="The number of pivots">
Number of Pivots
<output id="numPivotsSliderOutput">3</output><br/>
<input type="range" min="1" max="50" value="3" step="1" oninput="d3.select('#numPivotsSliderOutput').text(value); NUM_PIVOTS=value;">
</label>
</div>
</div>
<br/>
<label title="Number of iterations done at the end">
Full iterations
<output id="fullIterationsSliderOutput">20</output><br/>
<input type="range" min="1" max="100" value="20" step="1" oninput="d3.select('#fullIterationsSliderOutput').text(value); FULL_ITERATIONS=value;">
</label>
<br/>
<label title="NeighbourSize">
Neighbour Set
<output id="hlneighbourSizeSliderOutput">6</output><br/>
<input type="range" min="1" max="100" value="6" step="1" oninput="d3.select('#hlneighbourSizeSliderOutput').text(value); NEIGHBOUR_SIZE=value;">
</label>
<br/>
<label title="SampleSize">
Sample Set
<output id="hlsampleSizeSliderOutput">3</output><br/>
<input type="range" min="1" max="100" value="3" step="1" oninput="d3.select('#hlsampleSizeSliderOutput').text(value); SAMPLE_SIZE=value;">
</label>
</div>
<input id="NSButton" type="radio" name="algorithm" onclick="d3.select('#startSimulation').on('click', startNeighbourSamplingSimulation)">Neighbour
and Sampling<br>
<div id="NSParameters" class="parameters" style="display:none">
<label title="NeighbourSize">
Neighbour Set
<output id="neighbourSizeSliderOutput">6</output><br/>
<input type="range" min="1" max="100" value="6" step="1" oninput="d3.select('#neighbourSizeSliderOutput').text(value); NEIGHBOUR_SIZE=value;">
</label>
<br/>
<label title="SampleSize">
Sample Set
<output id="sampleSizeSliderOutput">3</output><br/>
<input type="range" min="1" max="100" value="3" step="1" oninput="d3.select('#sampleSizeSliderOutput').text(value); SAMPLE_SIZE=value;">
</label>
</div>
<input class="noParameters" type="radio" name="algorithm" onclick="d3.select('#startSimulation').on('click', startLinkSimulation)">Link
force in D3<br>
<input class="noParameters" type="radio" name="algorithm" onclick="d3.select('#startSimulation').on('click', startBarnesHutSimulation)">Barnes-Hut<br>
<input id="tSNEButton" type="radio" name="algorithm" onclick="d3.select('#startSimulation').on('click', starttSNE)">t-SNE<br>
<div id="tSNEParameters" class="parameters" style="display:none">
<label title="Perplexity">
Perplexity
<output id="perplexitySliderOutput">30</output><br/>
<input type="range" min="1" max="500" value="30" step="1" oninput="d3.select('#perplexitySliderOutput').text(value); PERPLEXITY=value;">
</label>
<br/>
<label title="LearningRate">
Learning Rate
<output id="learningRateSliderOutput">10</output><br/>
<input type="range" min="1" max="500" value="10" step="1" oninput="d3.select('#learningRateSliderOutput').text(value); LEARNING_RATE=value;">
</label>
</div>
</div>
</div>
<div class="left">
<p>Select distance function:</p>
<div id="distance">
<input type="radio" name="distance" onclick="distanceFunction=calculateDistance"> General<br>
<input type="radio" name="distance" onclick="distanceFunction=calculateEuclideanDistance"> Euclidean<br>
<input type="radio" name="distance" onclick="distanceFunction=calculateManhattanDistance"> Manhattan<br>
<input type="radio" name="distance" onclick="distanceFunction=calculateJaccardDissimilarity"> Jaccard<br>
<input type="radio" name="distance" onclick="distanceFunction=calculateDiceDissimilarity"> Dice<br>
<input type="radio" name="distance" onclick="distanceFunction=calculateCosineSimilarity"> Cosine<br>
<input type="radio" name="distance" onclick="distanceFunction=calculateDistancePoker"> Poker Hands<br>
</div>
</div>
</svg>
</body>
<!-- Load the files and libraries used. -->
<script src="js/lib/d3.v4.min.js"></script>
<script src="js/lib/papaparse.js"></script>
<script src="js/lib/jquery-3.1.1.js"></script>
<script src="js/lib/intercom.js"></script>
<script src="../build/d3-neighbour-sampling.js"></script>
<script src="js/src/neighbourSampling-papaparsing-nist-images.js"></script>
<script src="js/distances/distancePokerHands.js"></script>
<script src="js/distances/distance.js"></script>
<script src="js/distances/euclideanDistance.js"></script>
<script src="js/distances/euclideanDistanceInTSNE.js"></script>
<script src="js/distances/manhattanDistance.js"></script>
<script src="js/distances/jaccardDissimilarity.js"></script>
<script src="js/distances/diceDissimilarity.js"></script>
<script src="js/distances/cosineSimilarity.js"></script>
<script src="js/distances/normalization.js"></script>
<script src="js/distances/numeric.js"></script>
<script>
$(document).ready(function () {
$("#csv-file").change(function (d) {
parseFile(d);
$("#color_attr option").remove();
});
$("#tSNEButton").click(function () {
$(".parameters").hide();
$("#tSNEParameters").show();
});
$("#NSButton").click(function () {
$(".parameters").hide();
$("#NSParameters").show();
});
$("#HLButton").click(function () {
$(".parameters").hide();
$("#HLParameters").show();
if ($("#PButton").is(":checked")) {
$("#numPivots").show();
}
});
$("#BFButton").click(function () {
$("#numPivots").hide();
});
$("#PButton").click(function () {
$("#numPivots").show();
});
$(".noParameters").click(function () {
$(".parameters").hide();
});
});
</script>
</html>