update to final NEST 3.0 syntax

multiarea_model/simulation.py

@@ -622,6 +622,7 @@ def connect(simulation,
     source_area : Area instance
         Source area of the projection
     """
+
     network = simulation.network
     synapses = extract_area_dict(network.synapses,
                                  network.structure,
@@ -635,6 +636,50 @@ def connect(simulation,
                              network.structure,
                              target_area.name,
                              source_area.name)
+
+    if network.params['USING_NEST_3']:
+        for target in target_area.populations:
+            for source in source_area.populations:
+                conn_spec = {'rule': 'fixed_total_number',
+                             'N': int(synapses[target][source])}
+
+                if target_area == source_area:
+                    if 'E' in source:
+                        w_min = 0.
+                        w_max = np.Inf
+                        mean_delay = network.params['delay_params']['delay_e']
+                    elif 'I' in source:
+                        w_min = np.NINF
+                        w_max = 0.
+                        mean_delay = network.params['delay_params']['delay_i']
+                else:
+                    w_min = 0.
+                    w_max = np.Inf
+                    v = network.params['delay_params']['interarea_speed']
+                    s = network.distances[target_area.name][source_area.name]
+                    mean_delay = s / v
+
+                syn_spec = {
+                    'synapse_model': 'static_synapse',
+                    'weight': nest.math.redraw(
+                        nest.random.normal(mean=W[target][source],
+                                           std=W_sd[target][source]),
+                                           min=w_min,
+                                           max=w_max),
+                    'delay': nest.math.redraw(
+                        nest.random.normal(
+                            mean=mean_delay,
+                            std=(mean_delay *
+                                 network.params['delay_params']['delay_rel'])),
+                            min=simulation.params['dt'],
+                            max=np.Inf)
+                    }
+
+                nest.Connect(source_area.gids[source],
+                             target_area.gids[target],
+                             conn_spec,
+                             syn_spec)
+    else:
         for target in target_area.populations:
             for source in source_area.populations:
                 conn_spec = {'rule': 'fixed_total_number',
@@ -654,7 +699,6 @@ def connect(simulation,
                     v = network.params['delay_params']['interarea_speed']
                     s = network.distances[target_area.name][source_area.name]
                     mean_delay = s / v
-
                 syn_delay = {'distribution': 'normal_clipped',
                              'low': simulation.params['dt'],
                              'mu': mean_delay,
@@ -663,12 +707,6 @@ def connect(simulation,
                             'delay': syn_delay,
                             'model': 'static_synapse'}
 
-            if network.params['USING_NEST_3']:
-                nest.Connect(source_area.gids[source],
-                             target_area.gids[target],
-                             conn_spec,
-                             syn_spec)
-            else:
                 nest.Connect(tuple(range(source_area.gids[source][0],
                                          source_area.gids[source][1] + 1)),
                              tuple(range(target_area.gids[target][0],