Difference between revisions of "Team:TUDelft/js/plotfit"
| Line 114: | Line 114: | ||
pos_r[i+k] = r_sq(logistic, minimiser.solution, N, t); | pos_r[i+k] = r_sq(logistic, minimiser.solution, N, t); | ||
} catch (err) { | } catch (err) { | ||
| − | + | pos_r[i+k] = 0; | |
| + | Warning(err); | ||
} | } | ||
} | } | ||
| Line 155: | Line 156: | ||
var minimiser = numeric.uncmin(objective, initial); | var minimiser = numeric.uncmin(objective, initial); | ||
} catch (err) { | } catch (err) { | ||
| − | + | Warning("cannot find r: " + err); | |
| + | return 2; | ||
} | } | ||
return minimiser.solution[0]; | return minimiser.solution[0]; | ||
Latest revision as of 01:43, 2 November 2017
function plot(params) {
$("main.container").addClass("progress");
progress(params, plot);
// ################ // The rest defines the functions: // ################
// Gets data from form and validates.
function progress(params, plot) {
// Print an error
// Empty alert box and results box
$('#alert').html("");
$('#results').html("");
Message("Processing...");
// Getting all the data from the form.
var data = params.data.value.trim();
var thousands_seperator = params.thousands_seperator.value;
var thousands_checked = params.thousands_usage.checked;
var value_seperator = params.value_seperator.value;
var decimal_seperator = params.decimal_seperator.value;
if (value_seperator === 't') value_seperator = '\t';
Message("Validating format...");
// validation and manipulation
if (thousands_checked) {
if (thousands_seperator == value_seperator) {
Warning("Your thousands seperator is the same as the value seperator.");
}
if (thousands_seperator == decimal_seperator) {
Warning("Your thousands seperator is the same as the value seperator.");
}
data = replaceAll(data, thousands_seperator, );
}
if (value_seperator == decimal_seperator) {
return Error("Your value seperator is the same as the decimal seperator.");
}
// turn value seperator into ',' and decimal seperator into '.', and preventing those to be mixed up.
if (data.indexOf('¬') === -1) {
dataWithStrange = replaceAll(data, value_seperator, '¬');
dataDecimalToPoint = replaceAll(dataWithStrange, decimal_seperator, '.');
data = replaceAll(dataDecimalToPoint, '¬', ',');
} else {
return Error("¬ cannot be used as delimiter.");
}
data = replaceAll(data, "\"", "");
Message("Parsing...");
aa = numeric.parseCSV(data);
Message("Validating data...")
aa[0] = aa[0].filter(filterExceptZero);
aa[1] = aa[1].filter(filterExceptZero);
if (aa.length > 2) {
aa = numeric.transpose(aa);
}
if (aa.length !== 2) {
return Error("Enter data with 2 columns or rows.");
}
if (aa[0].length !== aa[1].length) {
Warning("Your two columns or rows are of different length. The longest one is truncated to match the other.");
var min = Math.min(aa[0].length, aa[1].length);
if (aa[0].length == min) {
aa[1] = aa[1].slice(0, min);
} else {
aa[0] = aa[0].slice(0, min);
}
}
aa = [aa[0], aa[1]];
aa = numeric.transpose(aa);
DATA = numeric.transpose(aa);
Message("Plotting...");
plot(aa, fit);
}
// Plots the data
function plot(data, fit) {
result("Your data has size " + data.length + ".");
$.plot($("#placeholder"), [{
color: 'yellow',
data: data
}]);
fit(data, plotfit);
}
function fit(data, plotfit) {
data = numeric.transpose(data);
var t = data[0];
var N = data[1];
var r = find_r(t, N);
var objective = makeObjective(logistic, t, N);
var possible_K = [0.5, 1, 1.5];
var possible_r = [0.9, 1, 1.1];
var pos_min = new Array(6);
var pos_r = new Array(6);
for (var i = 0; i < 3; i++) {
pre_K = possible_K[i];
for (var k = 0; k < 3; k++) {
pre_r = possible_r[k];
var initial = [N[0], pre_K * N[N.length - 1], pre_r * r];
try {
var minimiser = numeric.uncmin(objective, initial);
pos_min[i+k] = minimiser;
pos_r[i+k] = r_sq(logistic, minimiser.solution, N, t);
} catch (err) {
pos_r[i+k] = 0;
Warning(err);
}
}
}
console.log(pos_r);
var indexOfMaxValue = pos_r.reduce((iMax, x, i, arr) => x > arr[iMax] ? i : iMax, 0);
minimiser = pos_min[indexOfMaxValue];
result("Solution found after " + minimiser.iterations + " iterations.");
let r2 = r_sq(logistic, minimiser.solution, N, t);
result("With an R squared of " + r2 + ".");
result(minimiser.message);
draw(minimiser.solution);
var t = numeric.linspace(t[0], t[t.length - 1], t.length);
var N = vectorize(setParamInFunc(minimiser.solution, logistic), t);
// var N = (func, x) - > {
// var res = Array(x.length);
// for (var i = 0; i < x.length; i++) {
// res[i] = func(x[i]);
// }
// return res;
// }((func, params) - > {
// return (x) - >
// return func(params, x);
// }, t);
var datafit = [t, N];
datafit = numeric.transpose(datafit);
data = numeric.transpose(data);
plotfit(datafit, data, callback);
}
FINDR = find_r;
function find_r(t, N) {
var K = Math.max(...N);
var N_N = vectorize(((N) => N/K), N);
var lijntje = vectorize(((N_N) =>Math.log(N_N/(1-N_N))), N_N);
lijntje = removeAfterInfinity(lijntje);
t = t.slice(0, lijntje.length);
var initial = [0.005, lijntje[0]];
var objective = makeObjective(line, t, lijntje);
try {
var minimiser = numeric.uncmin(objective, initial);
} catch (err) {
Warning("cannot find r: " + err);
return 2;
}
return minimiser.solution[0];
}
function r_sq(f, popt, ydata, xdata) {
let residuals = new Array(ydata.length);
for(var i = 0; i<ydata.length; i++) {
residuals[i] = ydata[i] - f(popt, xdata[i]);
}
var ss_res = 0;
for (var i = 0; i<residuals.length; i++) {
ss_res += Math.pow(residuals[i], 2);
}
let mean = ydata.reduce((a,b)=>a+b, 0) / ydata.length;
var ss_tot = 0;
for (var i = 0; i<ydata.length; i++) {
ss_tot += Math.pow(ydata[i] - mean, 2);
}
return 1 - (ss_res / ss_tot);
}
function removeAfterInfinity(arr) {
var res = [];
for (i=0; i<arr.length; i++) {
if (arr[i] !== Infinity) {
res.push(arr[i]);
} else {
return res;
}
}
}
// lijntje = line(params, t)
function line(params, t) {
var a, b;
[a, b] = params
return a*t + b;
}
function plotfit(datafit, data, callback) {
$.plot($("#placeholder"), [{
label: "fitted data",
data: datafit,
color: 'green'
}, {
label: "input data",
data: data,
color: 'yellow'
}], {
legend: {
position: "nw"
}
});
callback();
}
// Tells user we are done.
function callback() {
$("main.container").removeClass("progress");
}
// ################ // The following functions are out of the callback work loop // ################
// Decorator for functions to perform vectorized
function vectorize(func, x) {
var res = new Array(x.length);
for (var i = 0; i < x.length; i++) {
res[i] = func(x[i]);
}
return res;
}
// Decorator for functions to set params fixed
function setParamInFunc(params, func) {
function resFunc(x) {
return func(params, x);
}
return resFunc;
}
// Function to fit
// N = logistic(params,t);
function logistic(params, t) {
var N0, K, r, ans;
[N0, K, r] = params;
var below = (K + N0 * (Math.exp(r * t) - 1));
if (below === Infinity) {
ans = 0;
} else {
ans = (K * N0 * Math.exp(r * t)) / (K + N0 * (Math.exp(r * t) - 1));
}
return ans;
}
// Least square objective
// Build as factory with a decorator
function makeObjective(targetFunc, x, y) {
function objective(params) {
var total = 0.0
for (var i = 0; i < y.length; i++) {
var result = targetFunc(params, x[i])
var delta = result - y[i];
total += delta * delta;
}
return total;
}
return objective;
}
function draw(params) {
param_names = ["N0", "K", "r"];
for (var i = 0; i < param_names.length; i++) {
result(param_names[i] + " is " + params[i]);
}
var latex = katex.renderToString("N(t) = \\frac{K \\cdot N_0 \\cdot e^{rt}}{K + N_0 \\cdot (e^{rt}-1)}");
result("For the function:")
resultHTML(latex);
}
function result(e) {
$("#results").append($("<p />", {
class: "result",
text: e
}));
}
function resultHTML(e) {
$("#results").append($("<p />", {
class: "result",
html: e
}));
}
// Print an error (This function is usually returned.)
function Error(e) {
$("#alert").prepend($('<p />', {
class: 'error',
text: e
}));
$("main.container").removeClass("progress");
}
// Print a warming
function Warning(e) {
$("#alert").append($('<p />', {
class: 'warning',
text: e
}));
}
// Print a message
function Message(e) {
$("#alert").append($('<p />', {
class: 'message',
text: e
}));
}
// This functions takes a string and adds \ before any character that needs to be escaped in a regex.
// This is necesarry when putting user input into a regex.
function escapeRegExp(string) {
return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string
}
// This functions replaces all matched characters and also does this safe for user input
function replaceAll(str, find, replace) {
return str.replace(new RegExp(escapeRegExp(find), 'g'), replace);
}
// This function returns false when NaN, false, and undefined, but returns true for 0
function filterExceptZero(el) {
if (el === 0) return true;
else return Boolean(el);
}
}
