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JuliusHerrmann
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26
graphUtils.js
Normal file
26
graphUtils.js
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function edgelistToDot(name, inp){
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var output = "strict graph \"" + name + "\" {\n";
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for(e in inp){
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e = inp[e];
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output += e[0] + " -- " + e[1] + ";\n";
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}
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output += "}";
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return output;
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}
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function dotToEdgelist(graph){
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var outList = [];
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graph = graph.split("\n");
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//var name = graph[0].split(" ")[2];
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//name = name.slice(1, name.length - 1);
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for (var i = 0; i < graph.length - 1; i++){
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if(i == 0){
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continue;
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}
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var nodes = graph[i].split("--");
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var node1 = Number(nodes[0]);
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var node2 = Number(nodes[1].slice(0, nodes[1].length - 1));
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outList.push([node1, node2]);
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}
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return outList;
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}
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12
main.vue
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12
main.vue
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const Counter = {
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data() {
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return {
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counter: 0
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}
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},
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mounted(){
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}
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}
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Vue.createApp(Counter).mount('#counter')
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20
simulation.html
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20
simulation.html
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<!DOCTYPE html>
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<html>
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<head>
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<title>Simulation</title>
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</head>
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<body>
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<div id="counter">
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Counter: {{ counter }}
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</div>
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<!--Simulation libraries-->
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<script src="graphUtils.js"></script>
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<script src="simulation.js"></script>
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<!--Vue.js libraries-->
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<script src="https://unpkg.com/vue@next"></script>
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<!--logic-->
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<script src="main.vue"></script>
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</body>
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</html>
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203
simulation.js
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203
simulation.js
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states = ["S", "I", "R"];
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rules = [[ "I", "R", 1 ], // spontaneous rule I -> R with rate 1.0
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[ "R", "S", 0.7 ], // spontaneous rule R -> S with rate 0.7
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[ [ "I","S","I" ],[ "I","I","I" ], 0.8 ]]; // contact rule I+S -> I+I with rate 0.8
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simulation = []
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graph_as_edgelist = [[ 0, 4 ], [ 0, 1 ], [ 1, 5 ], [ 1, 2 ], [ 2, 6 ], [ 2, 3 ], [ 3, 7 ], [ 4, 8 ], [ 4, 5 ], [ 5, 9 ], [ 5, 6 ], [ 6, 10 ], [ 6, 7 ], [ 7, 11 ], [ 8, 12 ], [ 8, 9 ], [ 9, 13 ], [ 9, 10 ], [ 10, 14 ], [ 10, 11 ], [ 11, 15 ], [ 12, 13 ], [ 13, 14 ], [ 14, 15 ]];
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horizon = 20.0; // wie lange wird simuliert
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initial_distribution = [0.5, 0.5, 0.0]; // gleiche Reihenfolge wie states, musss zu rules passen und normalisiert werden
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timepoint_num = 101;
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function get_next_state(current_labels){
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fastes_firing_time = 10000000.0; //dummy
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firing_rule = null;
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firing_node = null;
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firing_edge = null;
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//if(current_labels == null)
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//iterate over nodes
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for(node in nodes){
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node = nodes[node];
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current_state = current_labels[node];
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for(rule in rules){
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rule = rules[rule];
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if(rule[0] instanceof Array){
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//is contact rule
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continue;
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}
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if(current_state == rule[0]){
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current_fireing_time = randomExponential(rule[2]);
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//addFiringTime(current_fireing_time);
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if(current_fireing_time < fastes_firing_time){
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fastes_firing_time = current_fireing_time;
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firing_rule = rule;
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firing_node = node;
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firing_edge = null;
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}
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}
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}
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}
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//iterate over edges
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for(edge in graph_as_edgelist){
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edge = graph_as_edgelist[edge];
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node1 = node2 = edge;
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current_state1 = current_labels[node1];
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current_state2 = current_labels[node2];
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for(rule in rules){
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rule = rules[rule];
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if(typeof rule[0] == typeof ""){
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//is spont. rule
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continue
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}
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if(current_state1 == rule[0][0] && current_state2 == rule[0][1] || current_state2 == rule[0][0] && current_state1 == rule[0][1]){
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current_fireing_time = randomExponential(rule[2]);
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if(current_fireing_time < fastes_firing_time){
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fastes_firing_time = current_fireing_time;
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firing_rule = rule;
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firing_node = null;
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firing_edge = edge;
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}
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}
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}
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}
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if(firing_rule == null){
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//no rule could fire
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return [null, fastes_firing_time]; //would happen anyway but still
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}
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//apply rule
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new_labels = Array.from(current_labels);
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if(firing_node != null){
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new_labels[firing_node] = firing_rule[1];
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return [new_labels, fastes_firing_time];
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}
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console.assert(firing_edge != null);
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change_node1 = firing_edge[0];
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change_node2 = firing_edge[1];
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//we have to check which node changes in which direction
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if(new_labels[change_node1] == firing_rule[0][0] && new_labels[change_node2] == firing_rule[0][1]){
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new_labels[change_node1] = firing_rule[1][0];
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new_labels[change_node2] = firing_rule[1][1];
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}else{
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new_labels[change_node1] = firing_rule[1][1];
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new_labels[change_node2] = firing_rule[1][0];
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}
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return [new_labels, fastes_firing_time];
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}
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function count_states(current_labels){
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counter = [states.length];
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simulation.push(current_labels);
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for(label in current_labels){
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label = current_labels[label];
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index = states[ label ];
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counter[index] += 1;
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}
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}
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function generateNodes(edgelist){
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allNodes = [];
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for(e in edgelist){
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e = edgelist[e];
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allNodes.push(e[0]);
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allNodes.push(e[1]);
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}
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//sort
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allNodes = allNodes.sort((a, b) => (a > b));
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//remove duplicates
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finalArray = [];
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var last = -1;
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for(var i = 0; i < allNodes.length; i ++){
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if(last == allNodes[i]){
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continue;
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}
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else{
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finalArray.push(allNodes[i])
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last = allNodes[i];
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}
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}
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return finalArray;
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}
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nodes = generateNodes(graph_as_edgelist);
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//setup
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timepoints_samples = linspace(0, horizon, timepoint_num);
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timepoints_samples_static = linspace(0, horizon, timepoint_num);
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current_labels = randomChoice(states, nodes.length, initial_distribution);
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global_clock = 0;
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labels = [];
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timepoints = [];
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state_counts = [];
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simulate(rules, states, initial_distribution);
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function simulate(newRules, newStates, newDistr){
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rules = newRules;
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states = newStates;
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initial_distribution = newDistr;
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while(timepoints_samples.length > 0){
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[new_labels, time_passed] = get_next_state(current_labels);
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global_clock += time_passed;
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while(timepoints_samples.length > 0 && global_clock > timepoints_samples[0]){
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labels.push(Array.from(current_labels));
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state_counts.push(count_states(current_labels));
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timepoints_samples = timepoints_samples.slice(1, timepoints_samples.length);
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}
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current_labels = new_labels;
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}
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console.log(simulation);
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}
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// np helper functions
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function randomExponential(rate){
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if(rate == 0){ return 10000000 }
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return -Math.log(Math.random()) / rate;
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}
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function linspace(start, end, num){
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console.assert(start < end);
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console.assert(num > 0);
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distance = (end - start) / (num - 1);
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current = start;
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out = [];
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while(current <= end){
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out.push(Math.round(current * 100) / 100);
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current += distance;
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}
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return out;
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}
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function randomChoice(states, num, distr){
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out = [];
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let s = distr.reduce((a,e) => a + e);
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for(var i = 0; i < num; i++){
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let r = Math.random() * s;
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out.push(states.find((_,i) => (r -= distr[i]) < 0));
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}
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return out;
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}
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//times = [];
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//function addFiringTime(time){
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//times.push(time);
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//}
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//
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//function getAv(){
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//var sum = 0;
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//for(t in times){
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//t = times[t];
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//sum += t;
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//}
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//return sum / times.length;
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//}
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//simulate();
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11
tsconfig.json
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11
tsconfig.json
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@ -0,0 +1,11 @@
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// tsconfig.json
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{
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"compilerOptions": {
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"target": "esnext",
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"module": "esnext",
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// this enables stricter inference for data properties on `this`
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"strict": true,
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"jsx": "preserve",
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"moduleResolution": "node"
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}
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}
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