Changeset 991 for trunk

Timestamp:

09/30/11 15:05:02 (8 months ago)

Author:

apdavison

Message:

Allow modifying parameters of CurrentSource objects after creation in pyNN.nest (patch from Jan Antolik)

Location:

trunk/src

Files:

• common.py (modified) (2 diffs)
• nest/__init__.py (modified) (2 diffs)
• nest/electrodes.py (modified) (4 diffs)
• nest/recording.py (modified) (1 diff)
• nest/simulator.py (modified) (1 diff)

trunk/src/common.py

@@ -571 +571 @@
                          self.label, parametername, value_array.shape,
                          value_array.min(), value_array.max())
-        except TypeError:  # min() and max() won't work for non-numeric values
+        except (TypeError,ValueError):  # min() and max() won't work for non-numeric values
             logger.debug("%s.tset('%s', non_numeric_array(shape=%s))",
                          self.label, parametername, value_array.shape)
@@ -885 +885 @@
             else:
                 raise Exception("A maximum of 3 dimensions is allowed. What do you think this is, string theory?")
-            size = reduce(operator.mul, size)
+            size = int(reduce(operator.mul, size)) # NEST doesn't like numpy.int, so to be safe we cast to Python int
         self.size = size
         self.label = label or 'population%d' % Population.nPop

trunk/src/nest/__init__.py

@@ -193 +193 @@
         # perhaps should check for that
         assert n > 0, 'n must be a positive integer'
+        n = int(n)
+        
         celltype = cellclass(cellparams)
         nest_model = celltype.nest_name[simulator.state.spike_precision]
@@ -325 +327 @@
         self.synapse_model = synapse_dynamics._get_nest_synapse_model("projection_%d" % Projection.nProj)
         Projection.nProj += 1
+        
         self.connection_manager = simulator.ConnectionManager(self.synapse_type,
                                                               self.synapse_model,

trunk/src/nest/electrodes.py

@@ -100 +100 @@
         """
         self._device = nest.Create('step_current_generator')
+        
+        self._set(times,amplitudes)
+
+
+    def _set(self, times, amplitudes):
+        """Set currents in existing current source.
+        Arguments:
+            times      -- list/array of times at which the injected current changes.
+            amplitudes -- list/array of current amplitudes to be injected at the
+                          times specified in `times`.
+                          
+        The injected current will be zero up until the first time in `times`. The
+        current will continue at the final value in `amplitudes` until the end
+        of the simulation.
+        """
         assert len(times) == len(amplitudes), "times and amplitudes must be the same size (len(times)=%d, len(amplitudes)=%d" % (len(times), len(amplitudes))
         try:
@@ -109 +124 @@
         except AttributeError:
             numpy.append(amplitudes, amplitudes[-1])
-        nest.SetStatus(self._device, {'amplitude_times': numpy.array(times, 'float'),
-                                      'amplitude_values': 1000.0*numpy.array(amplitudes, 'float')})
-        
-        
+        nest.SetStatus(self._device, {'amplitude_times': list(numpy.array(times, 'float')),
+                                      'amplitude_values':list(1000.0*numpy.array(amplitudes, 'float'))})
+
 class NoisyCurrentSource(CurrentSource):
     """A Gaussian "white" noise current source. The current amplitude changes at fixed
@@ -146 +160 @@
                      specified, a NumpyRNG is used.
         """
+        self._device = nest.Create('noise_generator')
+        self._set(mean, stdev, dt, start, stop, rng)
+
+    def _set(self, mean, stdev, dt=None, start=0.0, stop=None, rng=None):
         self.rng = rng or NumpyRNG()
         self.dt = dt or state.dt
@@ -155 +173 @@
         self.stdev = stdev
         if isinstance(rng, NativeRNG):
-            self._device = nest.Create('noise_generator')
             nest.SetStatus(self._device, {'mean': mean*1000.0,
                                            'std': stdev*1000.0,

trunk/src/nest/recording.py

@@ -271 +271 @@
         except ValueError:
             pass
+        
+        if self._device != None:
+              recorders_to_reset=[]
+              for recorder in self.population.recorders.values():
+                  if hasattr(recorder, "_device") and recorder._device == self._device:
+                     recorders_to_reset.append(recorder)
+              for recorder in recorders_to_reset:
+                  recorder._device = None 
         self._create_device()
 

trunk/src/nest/simulator.py

@@ -128 +128 @@
             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.SetStatus([gid], [parameters])
         except: # I can't seem to catch the NESTError that is raised, hence this roundabout way of doing it.