Changeset 1033

Timestamp:

12/14/11 10:39:33 (5 months ago)

Author:

apdavison

Message:

In neo_output branch, made some fixes to the nest backend to improve its behaviour on calling reset()

Location:

branches/neo_output

Files:

• examples/reset_example.py (modified) (2 diffs)
• src/nest/__init__.py (modified) (1 diff)
• src/nest/electrodes.py (modified) (2 diffs)
• src/nest/recording.py (modified) (2 diffs)
• src/nest/simulator.py (modified) (3 diffs)

branches/neo_output/examples/reset_example.py

@@ -3 +3 @@
 """
 
-import pyNN.neuron as sim  # can of course replace `neuron` with `nest`, `brian`, etc.
+from pyNN.utility import get_script_args
+#import pyNN.neuron as sim  # can of course replace `neuron` with `nest`, `brian`, etc.
+simulator_name = get_script_args(1)[0]  
+exec("import pyNN.%s as sim" % simulator_name)
 import matplotlib.pyplot as plt
 from quantities import nA
@@ -31 +34 @@
 plt.xlabel("Time (%s)" % vm.times.units._dimensionality)
 plt.ylabel("Membrane potential (%s)" % vm.units._dimensionality)
-plt.savefig("reset_example.png")
+plt.savefig("reset_example_%s.png" % simulator_name)

branches/neo_output/src/nest/__init__.py

@@ -189 +189 @@
     assembly_class = Assembly
 
+    def __init__(self, size, cellclass, cellparams=None, structure=None,
+                 label=None):
+        __doc__ = common.Population.__doc__
+        super(Population, self).__init__(size, cellclass, cellparams, structure, label)
+        self._simulator.populations.append(self)
+    
     def _get_view(self, selector, label=None):
         return PopulationView(self, selector, label)

branches/neo_output/src/nest/electrodes.py

@@ -46 +46 @@
             amplitude -- pulse amplitude in nA
         """
-        self.amplitude = amplitude
+        self._amplitude = amplitude
+        self._start = start
+        self._stop = stop
         self._device = nest.Create('dc_generator')
         nest.SetStatus(self._device, {'amplitude': 1000.0*self.amplitude,
@@ -52 +54 @@
         if stop:
             nest.SetStatus(self._device, {'stop': float(stop)})
+
+    def _set_amplitude(self, value):
+        self._amplitude = value
+        nest.SetStatus(self._device, {'amplitude': 1000.0*value})
+    amplitude = property(fget=lambda self: self._amplitude, fset=_set_amplitude)
+    
+    def _set_start(self, value):
+        self._start = value
+        nest.SetStatus(self._device, {'start': float(value)})
+    start = property(fget=lambda self: self._start, fset=_set_start)
+    
+    def _set_stop(self, value):
+        self._stop = value
+        if value is not None:
+            nest.SetStatus(self._device, {'stop': float(value)})
+    stop = property(fget=lambda self: self._stop, fset=_set_stop)
 
 

branches/neo_output/src/nest/recording.py

@@ -414 +414 @@
                 ids = self.filter_recorded(variable, filter_ids)
                 data = self._multimeter.get_data(variable, ids)
+                signal_array = numpy.vstack(data.values())
                 segment.analogsignalarrays.append(
                     neo.AnalogSignalArray(
-                        data.T,
+                        signal_array.T,
                         units=recording.UNITS_MAP.get(variable, 'dimensionless'),
                         t_start=simulator.state.t_start*pq.ms,
@@ -422 +423 @@
                         name=variable,
                         source_population=self.population.label,
-                        source_ids=numpy.fromiter(ids, dtype=int))
+                        source_ids=numpy.array(data.keys()))
                 )
         return segment

branches/neo_output/src/nest/simulator.py

@@ -37 +37 @@
 recording_devices = []
 recorders = set([])
+populations = [] # needed for reset
 
 global net
@@ -90 +91 @@
     """Advance the simulation for a certain time."""
     for device in recording_devices:
-        device.connect_to_cells()
+        if not device._connected:
+            device.connect_to_cells()
     if not state.running:
         simtime += state.dt # we simulate past the real time by one time step, otherwise NEST doesn't give us all the recorded data
@@ -97 +99 @@
     
 def reset():
+    global populations
     nest.ResetNetwork()
     nest.SetKernelStatus({'time': 0.0})
+    for p in populations:
+        for variable, initial_value in p.initial_values.items():
+            p._set_initial_value_array(variable, initial_value)
     state.running = False
     state.t_start = 0.0