Dumping results as option

config_copy.yml

@@ -1,6 +1,6 @@
 name: ControlModelM2_sim
-max_time: 100
+max_time: 15
-num_trials: 2
+num_trials: 1
 network_params:
   generator: barabasi_albert_graph
   n: 100

run.py

@@ -11,5 +11,5 @@ def run(model, params=None):
 
 
 if __name__ == "__main__":
-    soil = Model(dump=True)
+    soil = Model(dump=False)
     run(soil)

server.py

@@ -12,6 +12,7 @@ import logging
 import logging
 import threading
 import io
+import networkx as nx
 from datetime import timedelta
 from contextlib import contextmanager
 
@@ -88,7 +89,6 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
                 self.send_log('INFO.soil', 'Using config: {name}'.format(name=self.config['name']))
 
             self.name = self.config['name']
-
             self.run_simulation()
 
             settings = []
@@ -114,7 +114,7 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
                 logger.info('Trial {} requested!'.format(msg['data']))
             self.send_log('INFO.user', 'Trial {} requested!'.format(msg['data']))
             self.write_message({'type': 'get_trial',
-                'data': self.application.model.get_trial(self.name, msg['data']) })
+                'data': self.get_trial( int(msg['data'] )) })
 
         elif msg['type'] == 'run_simulation':
             self.send_log('INFO.soil', 'Running new simulation for {name}'.format(name=self.config['name']))
@@ -147,7 +147,7 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
     def run_simulation(self):
         # Run simulation and capture logs
         with self.logging(self.application.model.name):
-            self.application.model.run(self.config)
+            self.simulation = self.application.model.run(self.config)
 
         trials = []
         for i in range(self.config['num_trials']):
@@ -155,6 +155,10 @@ class SocketHandler(tornado.websocket.WebSocketHandler):
         self.write_message({'type': 'trials',
             'data': trials })
 
+    def get_trial(self, trial):
+        G = self.simulation[trial].history_to_graph()
+        return nx.node_link_data(G)
+
     @contextmanager
     def logging(self, logger):
         self.capture_logging = True

templates/js/socket.js

@@ -21,27 +21,27 @@ ws.onmessage = function(message) {
             break;
 
         case 'get_trial':
-            console.log(msg['data']);
+            //console.log(msg['data']);
-            GraphVisualization.import(convertJSON(msg['data']['graph']), msg['data']['models'], function() {
+            GraphVisualization.import(convertJSON(msg['data']), function() {
                 $('#load').hide();
                 reset_configuration();
                 set_configuration();
                 $('#home_menu').click(function() {
                     setTimeout(function() {
                         reset_timeline();
-                        set_timeline(msg['data']['graph']);
+                        set_timeline(msg['data']);
                     }, 1000);
                 });
                 reset_timeline();
-                set_timeline(msg['data']['graph']);
+                set_timeline(msg['data']);
             });
             $('#charts .chart').removeClass('no-data');
-            set_chart_nodes(msg['data']['graph'], chart_nodes)
+            set_chart_nodes(msg['data'], chart_nodes)
-            set_chart_attrs(msg['data']['graph'], chart_attrs, $('.config-item #properties').val())
+            set_chart_attrs(msg['data'], chart_attrs, $('.config-item #properties').val())
             $('.config-item #properties').change(function() {
                 chart_attrs.destroy();
                 chart_attrs = create_chart(width_chart, height_chart, 'Time', 'Attributes', '#chart_attrs');
-                set_chart_attrs(msg['data']['graph'], chart_attrs, $('.config-item #properties').val())
+                set_chart_attrs(msg['data'], chart_attrs, $('.config-item #properties').val())
             });
             break;
 

templates/js/template.js

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

templates/js/visualization.js

@@ -13,7 +13,8 @@
 
   // Private constants
   var focus_opacity = 0.1,
-      radius = 8;
+      radius = 8,
+      required_node = ['id', 'index', 'label', 'px', 'py', 'spells', 'weight', 'x', 'y'];
 
   // Private variables
   var width,
@@ -43,6 +44,13 @@
     return ( this > min && this <= max ) || ( min === 0 && this === 0 );
   };
 
+  Number.prototype.type = function() {
+    if ( typeof(this) === 'number' )
+      return ( Number.isInteger(this) ) ? 'int' :  'float';
+    else 
+      return false;
+  }
+
   var lastFocusNode;
   var _helpers = {
     set_node: function(node, property, time) {
@@ -118,6 +126,13 @@
       link.style('opacity', function(o) {
           return o.source.index == d.index || o.target.index == d.index ? 1 : focus_opacity;
       });
+    },
+    push_once: function(array, item, key) {
+    for (var i in array) {
+      if ( array[i][key] == item[key] ) return false;
+    }
+    array.push(item);
+    return true;
   }
   }
 
@@ -253,6 +268,22 @@
     self.GraphVisualization.statistics = statistics
   }
 
+  function get_models(graph) {
+
+    var models = { 'dynamic': [], 'static': [] }
+
+    graph['nodes'].forEach(function(node) {
+      for ( var att in node ) {
+        if (!required_node.includes(att)) {
+          if ( Array.isArray(node[att]) ) _helpers.push_once(models['dynamic'], { 'title': att, 'type': node[att][0][0].type() }, 'title');
+          else _helpers.push_once(models['static'], { 'title': att, 'type': typeof(node[att]) }, 'title');
+        }
+      }
+    });
+
+    return models;
+  }
+
 
   /**
    * Public API
@@ -287,24 +318,21 @@
    * A function that imports the graph and the attributes of all the nodes.
    *
    * @param   {object}    json          The json structure of the graph.
-   * @param   {object}    attributes    Definition of the attributes of the nodes 
-   *                                    (statics and dynamics).
    * @param   {object}    callback      A function called at the end.
    */
-  function importJSON(json, attributes, callback) {
+  function importJSON(json, callback) {
     reset()
     graph = json;
-    model = attributes;
 
     // Create the graph itself
     Graph();
 
     self.GraphVisualization.nodes = graph.nodes.length;
     self.GraphVisualization.links = graph.links.length;
-    self.GraphVisualization.model = model;
+    self.GraphVisualization.model = get_models(json);
 
     // Draw graph with default property and time for the first time
-    update_data(model.dynamic[0].title, 0);
+    update_data(self.GraphVisualization.model.dynamic[0].title, 0);
 
     if (callback) { callback(); }
   }

visualization.py

@@ -1,5 +1,4 @@
 import os
-import networkx as nx
 from server import VisualizationElement
 from soil.simulation import SoilSimulation
 from xml.etree import ElementTree
@@ -7,10 +6,11 @@ from xml.etree import ElementTree
 
 class Model():
 
-    def __init__(self, dump=True, dir_path='output'):
+    def __init__(self, dump=False, dir_path='output'):
         self.name = 'soil'
         self.dump = dump
         self.dir_path = dir_path
+        self.simulation = list()
 
     def run(self, config):
         name = config['name']
@@ -22,40 +22,11 @@ class Model():
 
         print('Dumping results to {} : {}'.format(sim.dir_path, sim.dump))
         
-        sim.run_simulation()
+        return sim.run_simulation()
-
-
-    def get_trial(self, name, trial):
-        graph = nx.read_gexf(os.path.join(self.dir_path, name, '{}_trial_{}.gexf'.format(name, trial)))
-
-        attributes = self.get_attributes(os.path.join(self.dir_path, name, '{}_trial_{}.gexf'.format(name, trial)))
-        json = {}
-        json['graph'] = nx.node_link_data(graph)
-        json['models'] = attributes
-        return json
 
     def reset(self):
         pass
 
-    def get_attributes(self, path_gexf):
-        attributes = {}
-        tree = ElementTree.parse(path_gexf)
-        root = tree.getroot()
-
-        ns = { 'gexf': 'http://www.gexf.net/1.2draft' }
-
-        for mode in root[0].findall('gexf:attributes', ns):
-            attributes[mode.attrib['mode']] = []
-            for attribute in mode:
-                values = {
-                    'id'    : attribute.attrib['id'],
-                    'title' : attribute.attrib['title'],
-                    'type'  : attribute.attrib['type']
-                }
-                attributes[mode.attrib['mode']].append(values)
-
-        return attributes
-
 
 class GraphVisualization(VisualizationElement):
     package_includes = []