Changeset 1019 for trunk

Timestamp:

11/29/11 16:30:45 (6 months ago)

Author:

pierre

Message:

Fix some minors bugs in the Brian backend. Note that there is a difference still in Brian and NEST that should be solved in order to have the brunel benchmark working. Don't know how neuron behaves. If SpikeSource? are generating several spikes within a time dt, they are queued by Brian, while delivered by NEST (by multiplication of the weight by a number proportional to the number of spikes). I ll see it with Dan here next week.

Location:

trunk/src

Files:

• brian/__init__.py (modified) (1 diff)
• brian/connectors.py (modified) (4 diffs)
• brian/standardmodels/synapses.py (modified) (1 diff)
• nemo/__init__.py (modified) (1 diff)

trunk/src/brian/__init__.py

@@ -258 +258 @@
         
         if self._plasticity_model != "static_synapse":
-            for key in self._brian_connections.keys:
+            for key in self._brian_connections.keys():
                 synapses = self._brian_connections[key]
                 if self._plasticity_model is "stdp_synapse": 

trunk/src/brian/connectors.py

@@ -82 +82 @@
         for count, tgt in enumerate(projection.pre.local_cells):
             connector._probabilistic_connect(tgt, 1)
-            self.progression(count)        
+            self.progression(count, projection._simulator.state.mpi_rank)      
     
 
@@ -94 +94 @@
         for count, tgt in enumerate(projection.pre.local_cells):
             connector._probabilistic_connect(tgt, self.p_connect)
-            self.progression(count)
+            self.progression(count, projection._simulator.state.mpi_rank)
             
 
@@ -112 +112 @@
                 proba = proba.astype(float)           
             connector._probabilistic_connect(tgt, proba, self.n_connections)
-            self.progression(count)
+            self.progression(count, projection._simulator.state.mpi_rank)
 
 class FastOneToOneConnector(OneToOneConnector):
@@ -140 +140 @@
                 # the float is in case the values are of type numpy.float64, which NEST chokes on
                 projection._divergent_connect(src, [tgt], float(w), float(d), homogeneous)
-                self.progression(count)
+                self.progression(count, projection._simulator.state.mpi_rank)
                 count += 1
         else:

trunk/src/brian/standardmodels/synapses.py

@@ -15 +15 @@
     
     def __init__(self, timing_dependence=None, weight_dependence=None,
-                 voltage_dependence=None, dendritic_delay_fraction=0.0):
+                 voltage_dependence=None, dendritic_delay_fraction=1.0):
         assert dendritic_delay_fraction == 0, """Brian does not currently support dendritic delays:
                                                  for the purpose of STDP calculations all delays
                                                  are assumed to be axonal."""
-        standardmodels.STDPMechanism.__init__(self, timing_dependence, weight_dependence,
-                                      voltage_dependence, dendritic_delay_fraction)
+        super(STDPMechanism, self).__init__(timing_dependence, weight_dependence,
+                                            voltage_dependence, dendritic_delay_fraction)
 
 

trunk/src/nemo/__init__.py

@@ -47 +47 @@
     simulator but not by others.
     """
+    if (timestep < 1):
+        raise Exception("It is not currently possible to have a timestep less than 1ms with this simulator")
+    if (min_delay < 1):
+        raise Exception("It is not currently possible to have a min_delay less than 1ms with this simulator")
+    
     common.setup(timestep, min_delay, max_delay, **extra_params)
     simulator.state = simulator._State(timestep, min_delay, max_delay)