json works now

visualizer/public/js/main.js

@@ -1,3 +1,6 @@
+// Put the real domain here
+var baseUrl = "http://localhost"
+
 var network;
 var simulationData;
 animationPlaying = false;
@@ -8,6 +11,34 @@ const stepSlider = document.querySelector('#stepRange');
 const stepField = document.querySelector('#stepField');
 const animationDurationSlider = document.querySelector('#animationDurationRange');
 const animationDurationField = document.querySelector('#animationDurationField');
+
+var selectedGraph;
+var horizon;
+var states;
+var initial_distribution;
+var rules;
+var colors;
+
+// Debuging
+//selectedGraph = "strict graph GraphHello {\n0 -- 1;\n1 -- 2;\n1 -- 3;\n}";
+//selectedGraph = "strict graph Default {\n0 -- 1;\n1 -- 2;\n2 -- 3;\n3 -- 4;\n4 -- 5;\n0 -- 5;\n0 -- 3;\n0 -- 4;\n0 -- 2;\n1 -- 4;\n1 -- 5;\n1 -- 6;\n3 -- 5;\n3 -- 6;\n3 -- 4;\n}"
+
+selectedGraph = "strict graph Default {\n0 -- 10;\n0 -- 1;\n1 -- 11;\n1 -- 2;\n2 -- 12;\n2 -- 3;\n3 -- 13;\n3 -- 4;\n4 -- 14;\n4 -- 5;\n5 -- 15;\n5 -- 6;\n6 -- 16;\n6 -- 7;\n7 -- 17;\n7 -- 8;\n8 -- 18;\n8 -- 9;\n9 -- 19;\n10 -- 20;\n10 -- 11;\n11 -- 21;\n11 -- 12;\n12 -- 22;\n12 -- 13;\n13 -- 23;\n13 -- 14;\n14 -- 24;\n14 -- 15;\n15 -- 25;\n15 -- 16;\n16 -- 26;\n16 -- 17;\n17 -- 27;\n17 -- 18;\n18 -- 28;\n18 -- 19;\n19 -- 29;\n20 -- 30;\n20 -- 21;\n21 -- 31;\n21 -- 22;\n22 -- 32;\n22 -- 23;\n23 -- 33;\n23 -- 24;\n24 -- 34;\n24 -- 25;\n25 -- 35;\n25 -- 26;\n26 -- 36;\n26 -- 27;\n27 -- 37;\n27 -- 28;\n28 -- 38;\n28 -- 29;\n29 -- 39;\n30 -- 40;\n30 -- 31;\n31 -- 41;\n31 -- 32;\n32 -- 42;\n32 -- 33;\n33 -- 43;\n33 -- 34;\n34 -- 44;\n34 -- 35;\n35 -- 45;\n35 -- 36;\n36 -- 46;\n36 -- 37;\n37 -- 47;\n37 -- 38;\n38 -- 48;\n38 -- 39;\n39 -- 49;\n40 -- 50;\n40 -- 41;\n41 -- 51;\n41 -- 42;\n42 -- 52;\n42 -- 43;\n43 -- 53;\n43 -- 44;\n44 -- 54;\n44 -- 45;\n45 -- 55;\n45 -- 46;\n46 -- 56;\n46 -- 47;\n47 -- 57;\n47 -- 48;\n48 -- 58;\n48 -- 49;\n49 -- 59;\n50 -- 60;\n50 -- 51;\n51 -- 61;\n51 -- 52;\n52 -- 62;\n52 -- 53;\n53 -- 63;\n53 -- 54;\n54 -- 64;\n54 -- 55;\n55 -- 65;\n55 -- 56;\n56 -- 66;\n56 -- 57;\n57 -- 67;\n57 -- 58;\n58 -- 68;\n58 -- 59;\n59 -- 69;\n60 -- 70;\n60 -- 61;\n61 -- 71;\n61 -- 62;\n62 -- 72;\n62 -- 63;\n63 -- 73;\n63 -- 64;\n64 -- 74;\n64 -- 65;\n65 -- 75;\n65 -- 66;\n66 -- 76;\n66 -- 67;\n67 -- 77;\n67 -- 68;\n68 -- 78;\n68 -- 69;\n69 -- 79;\n70 -- 80;\n70 -- 71;\n71 -- 81;\n71 -- 72;\n72 -- 82;\n72 -- 73;\n73 -- 83;\n73 -- 74;\n74 -- 84;\n74 -- 75;\n75 -- 85;\n75 -- 76;\n76 -- 86;\n76 -- 77;\n77 -- 87;\n77 -- 78;\n78 -- 88;\n78 -- 79;\n79 -- 89;\n80 -- 90;\n80 -- 81;\n81 -- 91;\n81 -- 82;\n82 -- 92;\n82 -- 83;\n83 -- 93;\n83 -- 84;\n84 -- 94;\n84 -- 85;\n85 -- 95;\n85 -- 86;\n86 -- 96;\n86 -- 87;\n87 -- 97;\n87 -- 88;\n88 -- 98;\n88 -- 89;\n89 -- 99;\n90 -- 91;\n91 -- 92;\n92 -- 93;\n93 -- 94;\n94 -- 95;\n95 -- 96;\n96 -- 97;\n97 -- 98;\n98 -- 99;}"
+
+horizon = 20.0;
+//states = ["S", "I", "R"];
+states = ["N", "I", "V"];
+//initial_distribution = [0.5, 0.5, 0];
+initial_distribution = [0.9, 0.1, 0];
+//rules = "I R 1.0 R S 0.7 I S I I I I 0.8";
+rules = "N V 0.1 I N I I 0.5 I I N I I I 0.9 I N 0.2";
+// S I R
+colors = {
+	"N" : "#000000",
+	"I" : "#ffffff",
+	"V" : "#75c44c"
+}
+
 function createGraphFromDot(dotString){
 	var parsedData = vis.parseDOTNetwork(dotString);
   // create a network
@@ -62,32 +93,37 @@ function createGraphFromDot(dotString){
 function visualizeOneStep(step){
 	for(i = 0; i < step.length; i++){
 		n = network.body.nodes[i];
-		//console.log(step[i])
-		if(step[i][0] == 0){
 		n.setOptions({
 			color:{
-					background: "#0000ff",
+				background: colors[step[i]]
 			}
 		});
-		}else{
-			n.setOptions({
-				color:{
-					background: "#ff0000",
-				}
-			});
-		}
 	}
 	network.redraw();
 }
 
 
 function getSimulation(){
-	fetch("http://localhost/simulate")
+	//prepare the json data
+	json = {
+		graph: selectedGraph,
+		horizon: horizon,
+		states: states,
+		initial_distribution : initial_distribution,
+		rules : rules
+	}
+
+	//combine url
+	url = baseUrl + "/simulate?data=" + JSON.stringify(json);
+
+	fetch(url)
 		.then(response => response.json())
 		.then(response =>{
+			console.log(response)
 			simulationData = response;
-			stepSlider.max = simulationData.steps - 1;
-			createGraphFromDot(simulationData.dotGraph);
+			stepSlider.max = simulationData.states.length - 1;
+			//createGraphFromDot(simulationData.dotGraph);
+			createGraphFromDot(json.graph);
 			visualizeOneStep(simulationData.states[0]);
 			//kelvin to celsius
 			//let temp = Math.ceil(response.main.temp - 273.15);
@@ -102,7 +138,7 @@ function playAnimation(){
 		//Play the animation
 		animationInterval = setInterval(function(){ 
 			//This is the animation routine
-			if(currentAnimationStep == simulationData.steps){
+			if(currentAnimationStep == simulationData.states.length - 1){
 				//At the end of animation
 				clearInterval(animationInterval);
 				animationPlaying = false;

visualizer/public/python/graphUtils.py

@@ -0,0 +1,21 @@
+def edgelistToDot(name, inp):
+    output = "strict graph \"" + name + "\" {\n"
+    for (x,y) in inp:
+        output += f" {x} -- {y};\n"
+
+    output += "}"
+    return output
+
+def dotToEdgelist(graph):
+    outStr = []
+    graph = graph.split("\n")
+    name = graph[0].split(" ")[2]
+    name = name[1:len(name) - 1]
+    for i in range(len(graph) - 1):
+        if(i == 0):
+            continue
+        nodes = graph[i].split("--")
+        node1 = int(nodes[0])
+        node2 = int(nodes[1][0:len(nodes[1]) - 1])
+        outStr.append((node1, node2,))
+    return (name, outStr)

visualizer/public/python/simulationAdvanced.py

@@ -0,0 +1,241 @@
+# example execution
+# python simulationAdvanced.py '{
+        # "graph": "strict graph GraphHello {\n0 -- 1;\n1 -- 2;\n1 -- 3;\n}",
+        # "horizon": 20.0,
+        # "states": ["S", "I", "R"],
+        # "initial_distribution": [0.5, 0.5, 0],
+        # "rules": "I R 1.0 R S 0.7 I S I I 0.8"
+# }'
+
+import numpy as np
+import sys
+import graphUtils
+import json
+# statesComp = ["S", "I", "R"]
+rulesComp = [("I", "R", 1.0), # spontaneous rule  I -> R with rate 1.0
+        ("R", "S", 0.7),  # spontaneous rule R -> S with rate 0.7
+        (("I","S","I"),("I","I","I"), 0.8)] # contact rule I+S -> I+I with rate 0.4
+
+simulation = []
+
+class Rule:
+    def __init__(self, ruleParts, probability):
+        self.ruleParts = ruleParts
+        self.probability = probability
+
+    def getString(self):
+        output = "("
+        for part in self.ruleParts:
+            output += f"({part.getFromState().getValue()}, {part.getToState().getValue()}), "
+        output = output[0:len(output)-2]
+        output += f"), {self.probability})"
+        return output
+    
+    def getOutput(self):
+        # index of to state is ruleParts / 2
+        toStateIndex = int(len(self.ruleParts) / 2)
+        fromTuple = []
+        toTuple = []
+        for i in range(toStateIndex):
+            fromTuple.append(self.ruleParts[i])
+            toTuple.append(self.ruleParts[i + toStateIndex])
+
+        if(len(fromTuple) > 1):
+            fromTuple = tuple(fromTuple)
+            toTuple = tuple(toTuple)
+            return (fromTuple, toTuple, self.probability,)
+        else:
+            return (fromTuple[0], toTuple[0], self.probability,)
+
+
+
+def parseState(string):
+    output = ""
+    i = 0
+    while(not(string[i].isdigit() or string[i] == " ")):
+        output += string[i]
+        i += 1
+    return (output, string[i+1:],)
+
+def parseRate(string):
+    output = ""
+    i = 0
+    while(not string[i] == " "):
+        output += string[i]
+        i += 1
+        if(i == len(string)):
+            break
+    return(float(output), string[i+1:])
+
+
+# Extract rules from string
+# example: "Inf Inf Inf R 0.8"
+def stringToRule(Input):
+    allRules = []
+    rulePartsBuffer = []
+    while(len(Input) > 0):
+        newString = parseState(Input)
+        rulePartsBuffer.append(newString[0])
+
+        # check if we are at the end
+        if(newString[1][0].isdigit()):
+            newString = parseRate(newString[1])
+            allRules.append(Rule(rulePartsBuffer.copy(), newString[0]))
+            rulePartsBuffer.clear()
+    
+        Input = newString[1]
+
+    output = []
+    for r in allRules:
+        output.append(r.getOutput())
+    return output
+
+def stringToStates(inp):
+    inp = inp.split(" ")
+    out = []
+    for s in inp:
+        out.append(s)
+    return out
+
+def stringToDistr(inp):
+    inp = inp.split(" ")
+    out = []
+    for i in inp:
+        out.append(float(i))
+    return out
+
+# parse the input wohooooo
+# rules = stringToRule(sys.argv[1])
+# states = stringToStates(sys.argv[2])
+# initial_distribution = stringToDistr(sys.argv[3])
+
+jsonInput = json.loads(sys.argv[1])
+# print(jsonInput["graph"])
+graph_as_edgelist = graphUtils.dotToEdgelist(jsonInput["graph"])[1]
+horizon = jsonInput["horizon"]
+states = jsonInput["states"]
+initial_distribution = jsonInput["initial_distribution"]
+rules = stringToRule(jsonInput["rules"])
+# print(graph_as_edgelist)
+
+
+#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)]
+
+# print(graphUtils.edgelistToDot("testGraph", graph_as_edgelist))
+# print(graphUtils.dotToEdgelist("strict graph 'testGraph' {\n0 -- 4;\n0 -- 1;\n1 -- 5;\n}")[0])
+
+# horizon = 20.0   # wie lange wird simuliert
+# initial_distribution = [0.5, 0.5, 0.0] # gleiche Reihenfolge wie states, musss zu rules passen und normalisiert werden
+timepoint_num = 101
+def get_next_state(current_labels):
+    fastes_firing_time = 10000000.0  #dummy
+    firing_rule = None
+    firing_node = None
+    firing_edge = None
+    
+    # iterate over nodes
+    for node in nodes:
+        current_state = current_labels[node]
+        for rule in rules:
+            if 'tuple' in str(type(rule[0])):
+                # is contact rule
+                continue
+            if current_state == rule[0]:
+                current_fireing_time = np.random.exponential(1.0/rule[2])
+                if current_fireing_time < fastes_firing_time:
+                    fastes_firing_time = current_fireing_time
+                    firing_rule = rule
+                    firing_node = node
+                    firing_edge = None
+                    
+        
+    # iterate over edges:
+    for edge in graph_as_edgelist:
+        node1, node2 = edge
+        current_state1 = current_labels[node1]
+        current_state2 = current_labels[node2]
+        for rule in rules:
+            if 'str' in str(type(rule[0])):
+                # is spont. rule
+                continue
+            if (current_state1 == rule[0][0] and current_state2 == rule[0][1]) or (current_state2 == rule[0][0] and current_state1 == rule[0][1]): 
+                current_fireing_time = np.random.exponential(1.0/rule[2])
+                if current_fireing_time < fastes_firing_time:
+                    fastes_firing_time = current_fireing_time
+                    firing_rule = rule
+                    firing_node = None
+                    firing_edge = edge
+                
+
+    if firing_rule is None:
+        # no rule could fire
+        return None, fastes_firing_time # would happen anyway but still
+    
+    # apply rule
+    new_labels = list(current_labels) # copy
+    
+    if firing_node is not None:
+        new_labels[firing_node] = firing_rule[1]
+        return new_labels, fastes_firing_time
+        
+    assert(firing_edge is not None)    
+    change_node1 = firing_edge[0]
+    change_node2 = firing_edge[1]
+    # we have to check which node changes in which direction
+    if new_labels[change_node1] == firing_rule[0][0] and new_labels[change_node2] == firing_rule[0][1]:
+        new_labels[change_node1] = firing_rule[1][0]
+        new_labels[change_node2] = firing_rule[1][1]
+    else:
+        new_labels[change_node1] = firing_rule[1][1]
+        new_labels[change_node2] = firing_rule[1][0]
+        
+
+    return new_labels, fastes_firing_time
+
+def count_states(current_labels):
+    counter = [0 for _ in states]
+    simulation.append(current_labels)
+    for label in current_labels:
+        index = states.index(label)
+        counter[index] += 1
+    return counter
+
+nodes = sorted(list(set([e[0] for e in graph_as_edgelist] + [e[1] for e in graph_as_edgelist])))
+assert(nodes == list(range(len(nodes)))) # nodes haben labels 0...<N-1>
+
+# setup
+timepoints_samples = np.linspace(0.0, horizon, timepoint_num)
+timepoints_samples_static = np.linspace(0.0, horizon, timepoint_num)
+initial_labels = list(np.random.choice(states, len(nodes), p=initial_distribution))
+current_labels = initial_labels
+global_clock = 0.0
+labels = list()
+timepoints = list()
+state_counts = list()
+
+
+# simulate
+while len(timepoints_samples) > 0:
+    new_labels, time_passed = get_next_state(current_labels)
+    global_clock += time_passed
+    while len(timepoints_samples) > 0 and global_clock > timepoints_samples[0]:
+        labels.append(list(current_labels))
+        state_counts.append(count_states(current_labels))
+        timepoints_samples = timepoints_samples[1:]
+    current_labels = new_labels
+    
+
+for l in simulation:
+    # print(l)
+    pass
+
+# if(rulesComp == rules):
+    # print("Rules were parsed correctly")
+# else:
+    # print("Rules were not parsed correctly")
+
+# prepare the output json file
+outputJson = {
+        "states": simulation
+        }
+print(json.dumps(outputJson))

visualizer/src/Controller/SimulationController.php

@@ -2,6 +2,7 @@
 
 namespace App\Controller;
 
+use Symfony\Component\HttpFoundation\Request;
 use Symfony\Bundle\FrameworkBundle\Controller\AbstractController;
 use Symfony\Component\HttpFoundation\Response;
 use Symfony\Component\Routing\Annotation\Route;
@@ -18,20 +19,43 @@ class SimulationController extends AbstractController
         ]);
     }
 		#[Route('/simulate', name: 'run_simulation')]
-    public function simulate(): Response
+		public function simulate(Request $request): Response
 		{
-			$process1 = new Process(['python3', 'python/simulation.py']);
-			//$process = new Process(['cat', 'python/graph.dot']);
-			$process1->run();
-			//$process->run();
+			$input = $request->query->get('data');
+			$process = new Process(['python3', 'python/simulationAdvanced.py', $input]);
+			//$process = new Process(['python3', 'python/simulationAdvanced.py', '{
+        //"graph": "strict graph GraphHello {\n0 -- 1;\n1 -- 2;\n1 -- 3;\n}",
+        //"horizon": 20.0,
+        //"states": ["S", "I", "R"],
+        //"initial_distribution": [0.5, 0.5, 0],
+        //"rules": "I R 1.0 R S 0.7 I S I I 0.8"
+//}']);
+			$process->run();
 
 			// executes after the command finishes
-			if (!$process1->isSuccessful()) {
-					throw new ProcessFailedException($process1);
+			if (!$process->isSuccessful()) {
+					throw new ProcessFailedException($process);
 			}
 
-			$output = $process1->getOutput();
+			$output = $process->getOutput();
 			$response = new Response($output);
 			return $response;
 		}
+    //#[Route('/simulate', name: 'run_simulation')]
+    //public function simulate(): Response
+    //{
+			//$process1 = new Process(['python3', 'python/simulation.py']);
+			////$process = new Process(['cat', 'python/graph.dot']);
+			//$process1->run();
+			////$process->run();
+//
+			//// executes after the command finishes
+			//if (!$process1->isSuccessful()) {
+					//throw new ProcessFailedException($process1);
+			//}
+//
+			//$output = $process1->getOutput();
+			//$response = new Response($output);
+			//return $response;
+    //}
 }