Changeset 1017 for trunk

Timestamp:

11/28/11 14:15:15 (6 months ago)

Author:

pierre

Message:

The IF_curr_exp benchmark is almost passed for Nemo when dt=1ms, even if some discrepancies are still there. Need to continue to explore. Bug in the recording of variables, since they are recorded twice

Location:

trunk/src/nemo

Files:

• __init__.py (modified) (2 diffs)
• recording.py (modified) (2 diffs)
• simulator.py (modified) (5 diffs)
• standardmodels/cells.py (modified) (2 diffs)

trunk/src/nemo/__init__.py

@@ -136 +136 @@
         elif isinstance(celltype, cells.IF_curr_exp):
             init = celltype.default_initial_values
-            for idx in self.all_cells:
-                ntype = simulator.state.net.add_neuron_type('IF_curr_exp')
+            for idx in self.all_cells:                
+                ntype = simulator.state.net.add_neuron_type('IF_curr_exp')               
                 simulator.state.net.add_neuron(ntype, int(idx),
                         params['v_rest'],
+                        params['v_reset'],
                         params['cm'],
-                        params['tau_m'],
+                        params['tau_m'],                    
                         params['t_refrac'],
                         params['tau_syn_E'],
                         params['tau_syn_I'],
-                        params['i_offset'],
-                        params['v_reset'],
                         params['v_thresh'],
-                        init['v'], 0., 0., 1000.)
+                        params['i_offset'],                        
+                        init['v'], 0., 0., -1.)
         else:            
             init = celltype.default_initial_values
@@ -162 +162 @@
         if not hasattr(value, "__len__"):
             value = value*numpy.ones((len(self),))
-
+        for cell, val in zip(self, value):
+            cell.set_initial_value(variable, val)
 
 class Projection(common.Projection):

trunk/src/nemo/recording.py

@@ -21 +21 @@
         __doc__ = recording.Recorder.__doc__
         recording.Recorder.__init__(self, variable, population, file)
-        simulator.recorder_list.append(self)
+        self._simulator.recorder_list.append(self)
         self.data  = {}    
-        self.times = []    
-    
+        self.times = []
+
     def record(self, ids):
         """Add the cells in `ids` to the set of recorded cells."""
@@ -46 +46 @@
     def _add_vm(self, time):
         for id in list(self.recorded):
-            self.data[id] += [simulator.state.sim.get_membrane_potential(int(id))]
+            self.data[id] += [self._simulator.state.sim.get_membrane_potential(int(id))]
         self.times += [time]
 

trunk/src/nemo/simulator.py

@@ -60 +60 @@
         self.simulation    = None
         self.stdp          = None
-        self.verbose       = True
+        self.verbose       = False
 
     def progressbar(self, N):
@@ -87 +87 @@
 
     def run(self, simtime):
+        
         self.simulation = nemo.Simulation(self.net, self.conf)
         if self.verbose:
@@ -111 +112 @@
                     spikes += [source]
             
-            #for currents in current_sources:
-            #    currents.
             fired = numpy.sort(self.sim.step(spikes, currents)) 
 
@@ -118 +117 @@
                 self.simulation.apply_stdp(1.0)
 
-            for recorder in recorder_list:
+            for recorder in recorder_list[1:]:
                 if recorder.variable is "spikes":
                     recorder._add_spike(fired, self.t)
@@ -179 +178 @@
             
     def set_initial_value(self, variable, value):
-        indices = self.celltype.indices.items()
+        indices = self.celltype.initial_indices
         if state.simulation is None:
             state.net.set_neuron_state(self, indices[variable], value) 

trunk/src/nemo/standardmodels/cells.py

@@ -41 +41 @@
 
     indices = {'a' : 0, 'b' : 1, 'c' : 2, 'd' : 3}
-
     initial_indices = {'u' : 0, 'v' : 1}
 
@@ -152 +151 @@
     indices = {
             'v_rest' : 0,
-            'cm' : 1,
-            'tau_m' : 2,
-            't_refrac' : 3,
-            'tau_syn_E' : 4,
-            'tau_syn_I' : 5,
-            'i_offset' : 6,
-            'v_reset' : 7,
-            'v_thresh' : 8
+            'cm' : 2,
+            'tau_m' : 3,
+            't_refrac' : 4,
+            'tau_syn_E' : 5,
+            'tau_syn_I' : 6,
+            'i_offset' : 8,
+            'v_reset' : 1,
+            'v_thresh' : 7
         }
+
     initial_indices = {'v' : 0}