Changeset 1026 for branches

Timestamp:

12/08/11 11:16:40 (6 months ago)

Author:

apdavison

Message:

In neo_output branch, fixed a bug when recording gsyn, re-added scaling and prepending of initial value for nest data

Location:

branches/neo_output/src

Files:

• nest/__init__.py (modified) (2 diffs)
• nest/recording.py (modified) (5 diffs)
• nest/simulator.py (modified) (1 diff)
• neuron/recording.py (modified) (2 diffs)
• standardmodels/cells.py (modified) (7 diffs)

branches/neo_output/src/nest/__init__.py

@@ -34 +34 @@
 NEST_SYNAPSE_TYPES = nest.Models(mtype='synapses')
 
-STATE_VARIABLE_MAP = {"v": "V_m", "w": "w"}
+STATE_VARIABLE_MAP = {"v": "V_m", "w": "w", "gsyn_exc": "g_ex",
+                      "gsyn_inh": "g_in"}
 logger = logging.getLogger("PyNN")
 
@@ -286 +287 @@
 
     def _set_initial_value_array(self, variable, value):
-        if variable in STATE_VARIABLE_MAP:
-            variable = STATE_VARIABLE_MAP[variable]
-        nest.SetStatus(self.local_cells.tolist(), variable, value)
+        variable = STATE_VARIABLE_MAP.get(variable, variable)
+        try:
+            nest.SetStatus(self.local_cells.tolist(), variable, value)
+        except nest.NESTError, e:
+            logger.warning("NEST does not allow setting an initial value for %s" % variable) # assuming this is an "Unused dictionary items" error - should really check
 
 

branches/neo_output/src/nest/recording.py

@@ -19 +19 @@
 VARIABLE_MAP = {'v': 'V_m', 'gsyn_exc': 'g_ex', 'gsyn_inh': 'g_in'}
 REVERSE_VARIABLE_MAP = dict((v,k) for k,v in VARIABLE_MAP.items())
+SCALE_FACTORS = {'v': 1, 'gsyn_exc': 0.001, 'gsyn_inh': 0.001}
 
 logger = logging.getLogger("PyNN")
@@ -55 +56 @@
         each neuron, ids as keys.
         """
+        scale_factor = SCALE_FACTORS.get(variable, 1)
+        nest_variable = VARIABLE_MAP.get(variable, variable)
         events = nest.GetStatus(self.device,'events')[0]
         ids = events['senders']
-        values = events[variable]
+        values = events[nest_variable] * scale_factor # I'm hoping numpy optimises for the case where scale_factor = 1, otherwise should avoid this multiplication in that case
         data = {}
         for id in desired_ids:
             data[id] = values[ids==id]
+            if variable != 'spikes':
+                initial_value = id.get_initial_value(variable)
+                data[id] = numpy.concatenate(([initial_value], data[id]))
         return data
-    
+
 
 class SpikeDetector(RecordingDevice):
@@ -115 +121 @@
         current_variables.add(VARIABLE_MAP.get(variable, variable))
         _set_status(self.device, {'record_from': list(current_variables)})
-    
-
 
 
@@ -416 +420 @@
                     for id in self.filter_recorded('spikes', filter_ids)]
             else:
-                data = self._multimeter.get_data(VARIABLE_MAP.get(variable, variable),
+                data = self._multimeter.get_data(variable,
                                                  self.filter_recorded(variable, filter_ids))
-                segment.analogsignals = [
+                segment.analogsignals.extend(
                     neo.AnalogSignal(data[id],
                                      units=recording.UNITS_MAP.get(variable, 'dimensionless'),
@@ -426 +430 @@
                                      source_population=self.population.label,
                                      source_id=int(id))
-                    for id in self.filter_recorded(variable, filter_ids)]
+                    for id in self.filter_recorded(variable, filter_ids))
         return segment
 

branches/neo_output/src/nest/simulator.py

@@ -126 +126 @@
             gid = self
         try:
-            #nest does not like numpy array and so we will convert them to lists whenever we encounter one
-            for key in parameters:
-                if type(parameters[key]) == numpy.ndarray:
-                   parameters[key] = parameters[key].tolist()
+            #nest does not like numpy array if numpy was not available when it was compiled, and so we will convert them to lists whenever we encounter one
+            # to avoid this inefficiency, would be better to check at import time that NEST has been built with numpy support and raise an Exception if it hasn't
+            for key in parameters:
+                if type(parameters[key]) == numpy.ndarray:
+                   parameters[key] = parameters[key].tolist()
             nest.SetStatus([gid], [parameters])
         except: # I can't seem to catch the NESTError that is raised, hence this roundabout way of doing it.

branches/neo_output/src/neuron/recording.py

@@ -145 +145 @@
                 else:
                     signal = lambda id: id._cell.traces[variable]
-                segment.analogsignals = [
+                segment.analogsignals.extend(
                     neo.AnalogSignal(get_signal(id), # assuming not using cvode, otherwise need to use IrregularlySampledAnalogSignal
                                      units=recording.UNITS_MAP.get(variable, 'dimensionless'),
@@ -153 +153 @@
                                      source_population=self.population.label,
                                      source_id=int(id))
-                    for id in self.filter_recorded(variable, filter_ids)
-                ]
+                    for id in self.filter_recorded(variable, filter_ids))
                 assert segment.analogsignals[0].t_stop - simulator.state.t*pq.ms < simulator.state.dt*pq.ms
                 # need to add `Unit` and `RecordingChannel` objects

branches/neo_output/src/standardmodels/cells.py

@@ -101 +101 @@
     default_initial_values = {
         'v': -65.0, #'v_rest',
+        'gsyn_exc': 0.0,
+        'gsyn_inh': 0.0,
     }
     
@@ -125 +127 @@
     default_initial_values = {
         'v': -65.0, #'v_rest',
+        'gsyn_exc': 0.0,
+        'gsyn_inh': 0.0,
     }
 
@@ -162 +166 @@
     default_initial_values = {
         'v': -65.0, #'v_rest',
+        'gsyn_exc': 0.0,
+        'gsyn_inh': 0.0,
     }
     
@@ -187 +193 @@
     default_initial_values = {
         'v': -65.0, #'v_rest',
+        'gsyn_exc': 0.0,
+        'gsyn_inh': 0.0,
     }
 
@@ -213 +221 @@
     default_initial_values = {
         'v': -65.0, #'v_rest',
+        'gsyn_exc': 0.0,
+        'gsyn_inh': 0.0,
     }
 
@@ -248 +258 @@
         'v': -65.0, #'v_rest',
         'w': 0.0,
+        'gsyn_exc': 0.0,
+        'gsyn_inh': 0.0,
     }
 
@@ -283 +295 @@
         'v': -65.0, #'v_rest',
         'w': 0.0,
+        'gsyn_exc': 0.0,
+        'gsyn_inh': 0.0,
     }