Colors and shapes

TerroristNetworkModel.py

@@ -0,0 +1,245 @@
+import random
+import networkx as nx
+from soil.agents import BaseAgent
+from scipy.spatial import cKDTree as KDTree
+
+global betweenness_centrality_global
+global degree_centrality_global
+
+betweenness_centrality_global = None
+degree_centrality_global = None
+
+class TerroristSpreadModel(BaseAgent):
+    """
+    Settings:
+        information_spread_intensity
+
+        terrorist_additional_influence
+
+        min_vulnerability (optional else zero)
+
+        max_vulnerability
+
+        prob_interaction
+    """
+
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+
+        global betweenness_centrality_global
+        global degree_centrality_global
+        
+        if betweenness_centrality_global == None:
+            betweenness_centrality_global = nx.betweenness_centrality(self.global_topology)
+        if degree_centrality_global == None:
+            degree_centrality_global = nx.degree_centrality(self.global_topology)
+
+        self.information_spread_intensity = environment.environment_params['information_spread_intensity']
+        self.terrorist_additional_influence = environment.environment_params['terrorist_additional_influence']
+        self.prob_interaction = environment.environment_params['prob_interaction']
+
+        if self.state['id'] == 0:       # Civilian
+            self.initial_belief = random.uniform(0.00, 0.5)
+        elif self.state['id'] == 1:     # Terrorist
+            self.initial_belief = random.uniform(0.8, 1.00)
+        elif self.state['id'] == 2:     # Leader
+            self.initial_belief = 1.00
+
+        if 'min_vulnerability' in environment.environment_params:
+            self.vulnerability = random.uniform( environment.environment_params['min_vulnerability'], environment.environment_params['max_vulnerability'] )
+        else :
+            self.vulnerability = random.uniform( 0, environment.environment_params['max_vulnerability'] )
+
+        self.mean_belief = self.initial_belief
+        self.betweenness_centrality = betweenness_centrality_global[self.id]
+        self.degree_centrality = degree_centrality_global[self.id]
+
+        # self.state['radicalism'] = self.mean_belief
+
+    def count_neighboring_agents(self, state_id=None):
+        if isinstance(state_id, list):
+            return len(self.get_neighboring_agents(state_id))
+        else:
+            return len(super().get_agents(state_id, limit_neighbors=True))
+
+    def get_neighboring_agents(self, state_id=None):
+        if isinstance(state_id, list):
+            _list = []
+            for i in state_id:
+                _list += super().get_agents(i, limit_neighbors=True)
+            return [ neighbour for neighbour in _list if isinstance(neighbour, TerroristSpreadModel) ]
+        else:
+            _list = super().get_agents(state_id, limit_neighbors=True) 
+            return [ neighbour for neighbour in _list if isinstance(neighbour, TerroristSpreadModel) ]
+
+    def step(self):
+        if self.state['id'] == 0:       # Civilian
+            self.civilian_behaviour()
+        elif self.state['id'] == 1:     # Terrorist
+            self.terrorist_behaviour()
+        elif self.state['id'] == 2:     # Leader
+            self.leader_behaviour()
+
+    def civilian_behaviour(self):
+        if self.count_neighboring_agents() > 0:
+            neighbours = []
+            for neighbour in self.get_neighboring_agents():
+                if random.random() < self.prob_interaction:
+                    neighbours.append(neighbour)
+            influence = sum( neighbour.degree_centrality for neighbour in neighbours )
+            mean_belief = sum( neighbour.mean_belief * neighbour.degree_centrality / influence for neighbour in neighbours )
+            self.initial_belief = self.mean_belief
+            mean_belief = mean_belief * self.information_spread_intensity + self.initial_belief * ( 1 - self.information_spread_intensity )
+            self.mean_belief = mean_belief * self.vulnerability + self.initial_belief * ( 1 - self.vulnerability )
+        
+        if self.mean_belief >= 0.8:
+            self.state['id'] = 1
+
+        # self.state['radicalism'] = self.mean_belief
+
+    def leader_behaviour(self):
+        self.mean_belief = self.mean_belief ** ( 1 - self.terrorist_additional_influence )
+        if self.count_neighboring_agents(state_id=[1,2]) > 0:
+            for neighbour in self.get_neighboring_agents(state_id=[1,2]):
+                if neighbour.betweenness_centrality > self.betweenness_centrality:
+                    self.state['id'] = 1
+
+        # self.state['radicalism'] = self.mean_belief
+
+    def terrorist_behaviour(self):
+        if self.count_neighboring_agents(state_id=[1,2]) > 0:
+            neighbours = self.get_neighboring_agents(state_id=[1,2])
+            influence = sum( neighbour.degree_centrality for neighbour in neighbours )
+            mean_belief = sum( neighbour.mean_belief * neighbour.degree_centrality / influence for neighbour in neighbours )
+            self.initial_belief = self.mean_belief
+            self.mean_belief = mean_belief * self.vulnerability + self.initial_belief * ( 1 - self.vulnerability )
+            self.mean_belief = self.mean_belief ** ( 1 - self.terrorist_additional_influence )
+
+        if self.count_neighboring_agents(state_id=2) == 0 and self.count_neighboring_agents(state_id=1) > 0:
+            max_betweenness_centrality = self
+            for neighbour in self.get_neighboring_agents(state_id=1):
+                if neighbour.betweenness_centrality > max_betweenness_centrality.betweenness_centrality:
+                    max_betweenness_centrality = neighbour
+            if max_betweenness_centrality == self:
+                self.state['id'] = 2
+
+        # self.state['radicalism'] = self.mean_belief
+
+    def add_edge(self, G, source, target):
+        G.add_edge(source.id, target.id, start=self.env._now)
+
+    def link_search(self, G, node, radius):
+        pos = nx.get_node_attributes(G, 'pos')
+        nodes, coords = list(zip(*pos.items()))
+        kdtree = KDTree(coords)  # Cannot provide generator.
+        edge_indexes = kdtree.query_pairs(radius, 2)
+        _list = [ edge[int(not edge.index(node))] for edge in edge_indexes if node in edge ]
+        return [ G.nodes()[index]['agent'] for index in _list ]
+
+    def social_search(self, G, node, steps):
+        nodes = list(nx.ego_graph(G, node, radius=steps).nodes())
+        nodes.remove(node)
+        return [ G.nodes()[index]['agent'] for index in nodes ]
+
+
+class TrainingAreaModel(BaseAgent):
+    """
+    Settings:
+        training_influence
+
+        min_vulnerability
+
+    Requires TerroristSpreadModel.
+    """
+
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        self.training_influence = environment.environment_params['training_influence']
+        if 'min_vulnerability' in environment.environment_params:
+            self.min_vulnerability = environment.environment_params['min_vulnerability']
+        else: self.min_vulnerability = 0
+
+    def step(self):
+        for neighbour in self.get_neighboring_agents():
+            if isinstance(neighbour, TerroristSpreadModel) and neighbour.vulnerability > self.min_vulnerability:
+                neighbour.vulnerability = neighbour.vulnerability * ( 1 - self.training_influence )
+
+
+class HavenModel(BaseAgent):
+    """
+    Settings:
+        haven_influence
+
+        max_vulnerability
+
+    Requires TerroristSpreadModel.
+    """
+
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+        self.haven_influence = environment.environment_params['haven_influence']
+        self.max_vulnerability = environment.environment_params['max_vulnerability']
+
+    def step(self):
+        if self.count_neighboring_agents(state_id=0) == 0:
+            self.state['id'] = 1       # Terrorism Haven
+        else:
+            self.state['id'] = 0       # Civilian Haven
+
+        for neighbour in self.get_neighboring_agents():
+            if isinstance(neighbour, TerroristSpreadModel) and neighbour.vulnerability < self.max_vulnerability:
+                neighbour.vulnerability = neighbour.vulnerability ** ( 1 - self.haven_influence )
+
+
+class TerroristNetworkModel(TerroristSpreadModel):
+    """
+    Settings:
+        sphere_influence
+
+        vision_range
+
+        weight_social_distance
+
+        weight_link_distance
+    """
+
+    def __init__(self, environment=None, agent_id=0, state=()):
+        super().__init__(environment=environment, agent_id=agent_id, state=state)
+
+        self.vision_range = environment.environment_params['vision_range']
+        self.sphere_influence = environment.environment_params['sphere_influence']
+        self.weight_social_distance = environment.environment_params['weight_social_distance']
+        self.weight_link_distance = environment.environment_params['weight_link_distance']
+
+    def step(self):
+        if self.state['id'] == 1 or self.state['id'] == 2:
+            self.update_relationships()
+        super().step()
+
+    def update_relationships(self):
+        if self.count_neighboring_agents(state_id=0) == 0:
+            close_ups = self.link_search(self.global_topology, self.id, self.vision_range)
+            step_neighbours = self.social_search(self.global_topology, self.id, self.sphere_influence)
+            search = list(set(close_ups).union(step_neighbours))
+            neighbours = self.get_neighboring_agents()
+            search = [item for item in search if not item in neighbours and isinstance(item, TerroristNetworkModel)]
+            for agent in search:
+                social_distance = 1 / self.shortest_path_length(self.global_topology, self.id, agent.id)
+                spatial_proximity = ( 1 - self.get_distance(self.global_topology, self.id, agent.id) )
+                prob_new_interaction = self.weight_social_distance * social_distance + self.weight_link_distance * spatial_proximity
+                if random.random() < prob_new_interaction:
+                    self.add_edge(self.global_topology, self, agent)
+                    break
+
+    def get_distance(self, G, source, target):
+        source_x, source_y = nx.get_node_attributes(G, 'pos')[source]
+        target_x, target_y = nx.get_node_attributes(G, 'pos')[target]
+        dx = abs( source_x - target_x )
+        dy = abs( source_y - target_y )
+        return ( dx ** 2 + dy ** 2 ) ** ( 1 / 2 )
+
+    def shortest_path_length(self, G, source, target):
+        try:
+            return nx.shortest_path_length(G, source, target)
+        except nx.NetworkXNoPath:
+            return float('inf')

TerroristNetworkModel.yml

@@ -0,0 +1,58 @@
+name: TerroristNetworkModel_sim
+load_module: TerroristNetworkModel
+max_time: 100
+num_trials: 1
+network_params:
+  generator: random_geometric_graph
+  radius: 0.2
+  # generator: geographical_threshold_graph
+  # theta: 20
+  n: 50
+network_agents:
+  - agent_type: TerroristNetworkModel
+    weight: 0.8
+    state:
+      id: 0 # Civilians
+  - agent_type: TerroristNetworkModel
+    weight: 0.1
+    state:
+      id: 2 # Leaders
+  - agent_type: TrainingAreaModel
+    weight: 0.05
+    state:
+      id: 2 # Terrorism
+  - agent_type: HavenModel
+    weight: 0.05
+    state:
+      id: 0 # Civilian
+
+environment_params:
+  # TerroristSpreadModel
+  information_spread_intensity: 0.7
+  terrorist_additional_influence: 0.035
+  max_vulnerability: 0.5
+  prob_interaction: 0.5
+
+  # TrainingAreaModel and HavenModel
+  training_influence: 0.20
+  haven_influence: 0.20
+
+  # TerroristNetworkModel
+  vision_range: 0.50
+  sphere_influence: 2
+  weight_social_distance: 0.035
+  weight_link_distance: 0.035
+
+visualization_params:
+  # Icons downloaded from https://www.iconfinder.com/
+  shape_property: agent
+  shapes:
+    TrainingAreaModel: target
+    HavenModel: home
+  colors:
+    - attr_id: 0
+      color: green
+    - attr_id: 1
+      color: red
+    - attr_id: 2
+      color: '#c16a6a'

server.py

@@ -86,6 +86,9 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
                 self.config = self.config[0]
                 self.send_log('INFO.soil', 'Using config: {name}'.format(name=self.config['name']))
 
+            if 'visualization_params' in self.config:
+                self.write_message({'type': 'visualization_params',
+                    'data': self.config['visualization_params']})
             self.name = self.config['name']
             self.run_simulation()
 
@@ -93,6 +96,8 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
             for key in self.config['environment_params']: 
                 if type(self.config['environment_params'][key]) == float:
                     setting_type = 'number'
+                elif type(self.config['environment_params'][key]) == int:
+                    setting_type = 'number'
                 elif type(self.config['environment_params'][key]) == bool:
                     setting_type = 'boolean'
                 else:
@@ -149,8 +154,15 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
 
     def run_simulation(self):
         # Run simulation and capture logs
+        if 'visualization_params' in self.config:
+            del self.config['visualization_params']
         with self.logging(self.application.model.name):
-            self.simulation = self.application.model.run(self.config)
+            try:
+                self.simulation = self.application.model.run(self.config)
+            except:
+                error = 'Something went wrong. Please, try again.'
+                self.write_message({'type': 'error',
+                    'error': error})
 
         trials = []
         for i in range(self.config['num_trials']):
@@ -232,5 +244,5 @@ class ModularServer(tornado.web.Application):
         url = 'http://127.0.0.1:{PORT}'.format(PORT=self.port)
         print('Interface starting at {url}'.format(url=url))
         self.listen(self.port)
-        webbrowser.open(url)
+        # webbrowser.open(url)
         tornado.ioloop.IOLoop.instance().start()

templates/css/main.css

@@ -183,6 +183,7 @@ hr {
   z-index: 5;
   height: 35px;
   padding: .5rem 1rem;
+  overflow: hidden;
   line-height: 1.5;
   color: #464a4c;
   pointer-events: none;

templates/img/svg/home.svg

@@ -0,0 +1 @@
+<?xml version="1.0" ?><svg height="1792" viewBox="0 0 1792 1792" width="1792" xmlns="http://www.w3.org/2000/svg"><path d="M1472 992v480q0 26-19 45t-45 19h-384v-384h-256v384h-384q-26 0-45-19t-19-45v-480q0-1 .5-3t.5-3l575-474 575 474q1 2 1 6zm223-69l-62 74q-8 9-21 11h-3q-13 0-21-7l-692-577-692 577q-12 8-24 7-13-2-21-11l-62-74q-8-10-7-23.5t11-21.5l719-599q32-26 76-26t76 26l244 204v-195q0-14 9-23t23-9h192q14 0 23 9t9 23v408l219 182q10 8 11 21.5t-7 23.5z"/></svg>

templates/img/svg/person.svg

@@ -0,0 +1 @@
+<?xml version="1.0" ?><!DOCTYPE svg  PUBLIC '-//W3C//DTD SVG 1.1//EN'  'http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd'><svg height="512px" id="Layer_1" style="enable-background:new 0 0 512 512;" version="1.1" viewBox="0 0 512 512" width="512px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><path d="M448,448c0,0,0-26.4-2.2-40.2c-1.8-10.9-16.9-25.3-81.1-48.9c-63.2-23.2-59.3-11.9-59.3-54.6c0-27.7,14.1-11.6,23.1-64.2  c3.5-20.7,6.3-6.9,13.9-40.1c4-17.4-2.7-18.7-1.9-27c0.8-8.3,1.6-15.7,3.1-32.7C345.4,119.3,325.9,64,256,64  c-69.9,0-89.4,55.3-87.5,76.4c1.5,16.9,2.3,24.4,3.1,32.7c0.8,8.3-5.9,9.6-1.9,27c7.6,33.1,10.4,19.3,13.9,40.1  c9,52.6,23.1,36.5,23.1,64.2c0,42.8,3.9,31.5-59.3,54.6c-64.2,23.5-79.4,38-81.1,48.9C64,421.6,64,448,64,448h192H448z"/></svg>

templates/img/svg/plus.svg

@@ -0,0 +1 @@
+<?xml version="1.0" ?><!DOCTYPE svg  PUBLIC '-//W3C//DTD SVG 1.0//EN'  'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd'><svg enable-background="new 0 0 91.8 92.6" id="Layer_1" version="1.0" viewBox="0 0 91.8 92.6" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><path d="M46.3,3.6c-23.5,0-42.5,19-42.5,42.5s19,42.5,42.5,42.5c23.5,0,42.5-19,42.5-42.5S69.8,3.6,46.3,3.6z   M72.8,52.9H53v19.8c0,2-1.6,3.6-3.6,3.6h-6.2c-2,0-3.6-1.6-3.6-3.6V52.9H19.8c-2,0-3.6-1.6-3.6-3.6v-6.2c0-2,1.6-3.6,3.6-3.6h19.8  V19.7c0-2,1.6-3.6,3.6-3.6h6.2c2,0,3.6,1.6,3.6,3.6v19.8h19.8c2,0,3.6,1.6,3.6,3.6v6.2C76.4,51.2,74.8,52.9,72.8,52.9z" fill="#1E1E1E"/></svg>

templates/img/svg/target.svg

@@ -0,0 +1 @@
+<?xml version="1.0" ?><svg height="16px" version="1.1" viewBox="0 0 16 16" width="16px" xmlns="http://www.w3.org/2000/svg" xmlns:sketch="http://www.bohemiancoding.com/sketch/ns" xmlns:xlink="http://www.w3.org/1999/xlink"><title/><defs/><g fill="none" fill-rule="evenodd" id="Icons with numbers" stroke="none" stroke-width="1"><g fill="#000000" id="Group" transform="translate(-192.000000, -192.000000)"><path d="M201,205.917042 C203.512502,205.49553 205.495527,203.512505 205.917042,201 L203,201 L203,199 L205.917042,199 C205.495527,196.487495 203.512502,194.50447 201,194.082958 L201,197 L199,197 L199,194.082958 C196.487498,194.50447 194.504473,196.487495 194.082958,199 L197,199 L197,201 L194.082958,201 C194.504473,203.512505 196.487498,205.49553 199,205.917042 L199,203 L201,203 Z M200,208 C195.581722,208 192,204.418278 192,200 C192,195.581722 195.581722,192 200,192 C204.418278,192 208,195.581722 208,200 C208,204.418278 204.418278,208 200,208 Z M200,208" id="Oval 163"/></g></g></svg>

templates/img/svg/time.svg

@@ -0,0 +1 @@
+<?xml version="1.0" ?><!DOCTYPE svg  PUBLIC '-//W3C//DTD SVG 1.1//EN'  'http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd'><svg enable-background="new 0 0 64 64" height="64px" id="Layer_1" version="1.1" viewBox="0 0 64 64" width="64px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M52.419,15.975c0,0,1.013,1.019,1.727,0.002l1.363-1.953c0.476-0.687-0.139-1.162-0.202-1.209    l-8.265-5.775H47.04c-0.509-0.354-0.847-0.139-1.024,0.06l-0.148,0.213l-1.259,1.802c-0.006,0.007-0.71,1.119,0.416,1.707v0.001    c1.61,0.792,4.563,2.462,7.392,5.158L52.419,15.975z" fill="#241F20"/></g><g><path d="M38.512,0.071H25.488c-1.011,0-1.839,0.812-1.839,1.839v1.518c0,1.026,0.828,1.854,1.839,1.854h0.644    v1.072c0.001,1.541,0.974,1.669,1.462,1.636c0.083-0.012,0.169-0.025,0.26-0.037c0.001,0,0.013-0.003,0.013-0.003L27.866,7.95    c1.734-0.237,4.605-0.464,7.898-0.045l0.002-0.003c0,0,2.109,0.391,2.103-1.549V5.281h0.644c1.012,0,1.839-0.827,1.839-1.854V1.91    C40.351,0.884,39.523,0.071,38.512,0.071z" fill="#241F20"/></g><path d="M32,10.301c-14.808,0-26.812,12.005-26.812,26.815c0,14.807,12.004,26.812,26.812,26.812   c14.809,0,26.812-12.006,26.812-26.812C58.812,22.306,46.809,10.301,32,10.301z M33.717,37.108   c-1.575,0.002-1.709-1.094-1.717-1.41V17.155c0.046-0.645,0.381-1.86,2.248-1.546c0.037,0.005,0.072,0.009,0.111,0.014   c0.12,0.02,0.233,0.036,0.32,0.043c5.44,0.764,17.373,4.302,18.864,20.343c-0.042,0.446-0.295,1.096-1.412,1.103   C42.529,37.085,36.454,37.097,33.717,37.108z" fill="#241F20"/></g></svg>

templates/index.html

@@ -104,7 +104,7 @@
         $('#simulation_modal .btn-success').click(function() {
             if ( !jQuery.isEmptyObject(run_simulation()) ) {
                 self.GraphVisualization.reset();
-                $('#load').show().addClass('loader');;
+                $('#load').show().addClass('loader');
                 _socket.send(run_simulation(), 'run_simulation');
                 $('.console').append('<br/>');
             }

templates/js/socket.js

@@ -15,15 +15,15 @@ ws.onmessage = function(message) {
 
     switch(msg['type']) {
         case 'trials':
-            $('#load').removeClass('loader');
             reset_trials();
             set_trials(msg['data']);
+            // $('#load').removeClass('loader');
             break;
 
         case 'get_trial':
             console.log(msg['data']);
-            GraphVisualization.import(convertJSON(msg['data']), function() {
+
-                $('#load').hide();
+            self.GraphVisualization.import(convertJSON(msg['data']), function() {
                 reset_configuration();
                 set_configuration();
                 $('#home_menu').click(function() {
@@ -34,6 +34,7 @@ ws.onmessage = function(message) {
                 });
                 reset_timeline();
                 set_timeline(msg['data']);
+                $('#load').hide();
             });
             $('#charts .chart').removeClass('no-data');
             set_chart_nodes(msg['data'], chart_nodes)
@@ -61,6 +62,11 @@ ws.onmessage = function(message) {
             $('.console').animate({ scrollTop: $('.console')[0].scrollHeight }, 'fast');
             break;
 
+        case 'visualization_params':
+            console.log(msg['data']);
+            self.GraphVisualization.set_params(msg['data']['shape_property'], msg['data']['shapes'], msg['data']['colors']);
+            break;
+
         default:
             console.log('Unexpected message!')
     }
@@ -103,6 +109,16 @@ var reset_trials = function() {
 }
 
 var convertJSON = function(json) {
+    // For NetworkX Geometric Graphs get positions
+    json.nodes.forEach(function(node) {
+        var scx = d3.scale.linear().domain([0, 1]).range([0, height]);
+        var scy = d3.scale.linear().domain([0, 1]).range([height, 0]);
+        if ( node.pos ) {
+            node.scx = scx(node.pos[0]);
+            node.scy = scy(node.pos[1]);
+        }
+        delete node.pos;
+    });
     json.links.forEach(function(link) {
         link.source = json.nodes[link.source]
         link.target = json.nodes[link.target]
@@ -136,7 +152,7 @@ var update_statistics_table = function() {
                                         statisticsSorted[i].split('.').pop().split('\'')[0] : statisticsSorted[i];
 
             $('<tr>').addClass('col-sm-12').appendTo('#percentTable > tbody');
-            $('<td>').css('background-color', self.GraphVisualization.color(statisticsSorted[i])).addClass('col-sm-1').appendTo(appendTo);
+            $('<td>').css('background-color', self.GraphVisualization.color($('.config-item #properties').val(), statisticsSorted[i])).addClass('col-sm-1').appendTo(appendTo);
             $('<td>').addClass('text-left col-sm-4').text(self.GraphVisualization.statistics[statisticsSorted[i]] + ' %').appendTo(appendTo);
             $('<td>').addClass('text-right col-sm-6 property-name').text(propertyName).appendTo(appendTo);
         }
@@ -211,6 +227,9 @@ var set_timeline = function(graph) {
     // Draw graph for the first time
     self.GraphVisualization.update_graph($('.config-item #properties').val(), maxUnix, function() {
         update_statistics_table();
+        setTimeout(function() {
+            self.GraphVisualization.fit();
+        }, 100);
     });
 
     // 'Speed' slider

templates/js/template.js

@@ -70,7 +70,7 @@ var initGUI = function(model_params) {
     };
 
     for (var option in model_params) {
-
+        
         var type = typeof(model_params[option]);
         var param_str = String(option);
 
@@ -82,7 +82,7 @@ var initGUI = function(model_params) {
                 addSliderInput(model_params[option]['label'], model_params[option]['value']);
                 break;
             default:
-                console.log(model_params[option]['type'] + ' not defined!');
+                console.log(model_params[option]['label'] + ' not defined!');
                 break;
         }
     }

templates/js/visualization.js

@@ -14,7 +14,7 @@
   // Private constants
   var focus_opacity = 0.1,
       radius = 8,
-      required_node = ['id', 'index', 'label', 'px', 'py', 'spells', 'weight', 'x', 'y'];
+      required_node = ['id', 'index', 'label', 'px', 'py', 'spells', 'weight', 'x', 'y', 'pos', 'scx', 'scy'];
 
   // Private variables
   var width,
@@ -35,7 +35,10 @@
       data_link,          // Actual link data for the graph
 
       link,               // Line svgs
-      node;               // Circles for the nodes
+      node,               // Circles for the nodes
+      shape_property,     // Property to whom the shape will be applied
+      shapes,             // Dictionary of shapes for nodes
+      colors;             // Dictionary of colors for nodes
 
   Number.prototype.between = function(min, max) {
     var min = (min || min === 0) ? min : Math.max(),
@@ -60,15 +63,29 @@
           .attr('r', radius)
           .style('fill', function (d) {
               if ( Array.isArray(d[property]) ) {
-                var color_node = color(d[property][0][0]);
+                var color_node = _helpers.set_color(property, d[property][0][0]);
                 d[property].forEach(function(p) {
-                  if ( time.between(p[1], p[2]) ) color_node = color(p[0]);
+                  if ( time.between(p[1], p[2]) ) color_node = _helpers.set_color(property, p[0]);
                 });
                 return color_node;
               } else {
-                return color(d[property]);
+                return _helpers.set_color(property, d[property]);
               }
           })
+          .style('stroke', function(d) {
+              if (_helpers.set_shape(d[shape_property]) !== (-1))
+                if ( Array.isArray(d[property]) ) {
+                  var color_node = _helpers.set_color(property, d[property][0][0]);
+                  d[property].forEach(function(p) {
+                    if ( time.between(p[1], p[2]) ) color_node = _helpers.set_color(property, p[0]);
+                  });
+                  return color_node;
+                } else {
+                  return _helpers.set_color(property, d[property]);
+                }
+              else 
+                return '#ffffff';
+          })
           // Cancel zoom movement so you can move the node
           .on('mousedown', function(d) {
               d3.event.stopPropagation();
@@ -93,16 +110,33 @@
       node.attr('class', 'node')
           .attr('r', radius)
           .style('fill', function (d) {
+              if (_helpers.set_shape(d[shape_property]) !== (-1)) {
+                return 'url(#' + _helpers.set_shape(d[shape_property]) + ')';
+              }
               if ( Array.isArray(d[property]) ) {
-                var color_node = color(d[property][0][0]);
+                var color_node = _helpers.set_color(property, d[property][0][0]);
                 d[property].forEach(function(p) {
-                  if ( time.between(p[1], p[2]) ) color_node = color(p[0]);
+                  if ( time.between(p[1], p[2]) ) color_node = _helpers.set_color(property, p[0]);
                 });
                 return color_node;
               } else {
-                return color(d[property]);
+                return _helpers.set_color(property, d[property]);
               }
           })
+          .style('stroke', function(d) {
+              if (_helpers.set_shape(d[shape_property]) !== (-1))
+                if ( Array.isArray(d[property]) ) {
+                  var color_node = _helpers.set_color(property, d[property][0][0]);
+                  d[property].forEach(function(p) {
+                    if ( time.between(p[1], p[2]) ) color_node = _helpers.set_color(property, p[0]);
+                  });
+                  return color_node;
+                } else {
+                  return _helpers.set_color(property, d[property]);
+                }
+              else 
+                return '#ffffff';
+          })
           .on('dblclick', function(d) {
             d3.event.stopPropagation();
             if (d === lastFocusNode) {
@@ -139,12 +173,33 @@
       });
     },
     push_once: function(array, item, key) {
-    for (var i in array) {
+      for (var i in array) {
-      if ( array[i][key] == item[key] ) return false;
+        if ( array[i][key] == item[key] ) return false;
+      }
+      array.push(item);
+      return true;
+    },
+    set_color: function(property, value) {
+      if ( colors instanceof Array ) {
+        for ( var c in colors ) {
+          if ( colors[c][property] == value ) { return colors[c]['color']; }
+        }
+        return color(value);
+      } else {
+        return color(value);
+      }
+    },
+    set_shape: function(value) {
+      if ( shapes instanceof Object && shape_property ) {
+        for ( var s in shapes ) {
+          var str_value = (value.includes('class')) ? value.split('.').pop().split('\'')[0] : value;
+          if ( str_value == s ) return shapes[s];
+        }
+        return (-1);
+      } else {
+        return (-1);
+      }
     }
-    array.push(item);
-    return true;
-  }
   }
 
 
@@ -170,6 +225,29 @@
     glinks = groot.append('g')  .attr('id', 'links');
     gnodes = groot.append('g')  .attr('id', 'nodes');
 
+    // Add patterns for shapes
+    var defs = [];
+    for ( var i in shapes )
+      if (!defs.includes(shapes[i])) defs.push(shapes[i])
+    
+    svg.append('defs')
+       .selectAll('pattern')
+       .data(defs)
+       .enter()
+       .append('pattern')
+       .attr('id', function(d, i) {
+          return d;
+       })
+       .attr('patternUnits', 'objectBoundingBox')
+       .attr('width', 1)
+       .attr('height', 1)
+       .append('image')
+       .attr('href', function(d) {
+          return window.location.protocol + '//' + window.location.host + '/img/svg/' + d + '.svg';
+       })
+       .attr('width', 16)
+       .attr('height', 16);
+
     // Zoom
     zoom = d3.behavior
              .zoom()
@@ -200,17 +278,22 @@
     force.on('tick', function () {
 
         link.attr('x1', function (d) {
-            return d.source.x;
+            if ( d.source.scx ) return d.source.scx;
+            else return d.source.x;
         }).attr('y1', function (d) {
-            return d.source.y;
+            if ( d.source.scy ) return d.source.scy;
+            else return d.source.y;
         }).attr('x2', function (d) {
-            return d.target.x;
+            if ( d.target.scx ) return d.target.scx;
+            else return d.target.x;
         }).attr('y2', function (d) {
-            return d.target.y;
+            if ( d.target.scy ) return d.target.scy;
+            else return d.target.y;
         });
 
         node.attr('transform',  function translate(d) {
-            return 'translate(' + d.x + ',' + d.y + ')';
+            if ( d.scx || d.scy ) return 'translate(' + d.scx + ',' + d.scy + ')';
+            else return 'translate(' + d.x + ',' + d.y + ')';
         });
     });
 
@@ -384,6 +467,25 @@
     }
   }
 
+  /**
+   * Set shapes and color of graph.
+   * A function that set the shapes and colors of the nodes depending on their status.
+   *
+   * @param   {object}    set_shapes    Shapes for nodes.
+   * @param   {object}    set_colors    Colors for nodes.
+   * @param   {object}    callback      A function called at the end.
+   */
+  function set_params(set_shape_property, set_shapes, set_colors, callback) {
+    shape_property = set_shape_property;
+    shapes = set_shapes;
+    colors = set_colors;
+
+    self.GraphVisualization.shapes = shapes;
+    self.GraphVisualization.colors = colors;
+
+    if (callback) { callback(); }
+  }  
+
   /**
    * Adjust the graph to the whole area.
    * A function that adjust the graph to the svg item.
@@ -437,9 +539,9 @@
    * @param   {object}    value         Value.
    * @return  {object}    color         The color in hexadecimal.
    */
-  function color(value) {
+  function color(property, value) {
     if (graph) {
-      return color(value);
+      return _helpers.set_color(property, value);
     }
   }
 
@@ -519,6 +621,7 @@
     create: create,
     import: importJSON,
     update_graph: update_graph,
+    set_params: set_params,
     set_link_distance: set_link_distance,
     fit: zoom_to_fit,
     reset: reset,
@@ -530,6 +633,8 @@
 
     // Getters
     color: color,
+    shapes: shapes,
+    colors: colors,
     get_attributes: get_attributes,
     get_nodes: get_nodes,
 

visualization.py

@@ -1,4 +1,5 @@
 import os
+import networkx as nx
 from server import VisualizationElement
 from soil.simulation import SoilSimulation
 from xml.etree import ElementTree
@@ -22,7 +23,16 @@ class Model():
 
         print('Dumping results to {} : {}'.format(sim.dir_path, sim.dump))
         
-        return sim.run_simulation()
+        simulation_results = sim.run_simulation()
+
+        G = simulation_results[0].history_to_graph()
+        for node in G.nodes():
+            if 'pos' in G.node[node]:
+                G.node[node]['viz'] = {"position": {"x": G.node[node]['pos'][0], "y": G.node[node]['pos'][1], "z": 0.0}}
+                del (G.node[node]['pos'])
+        nx.write_gexf(G, 'test.gexf', version='1.2draft')
+
+        return simulation_results
 
     def reset(self):
         pass