Changeset 436

Timestamp:

08/10/08 12:31:00 (3 months ago)

Author:

pierre

Message:

Add the possibility of having delays for SpikeSourceArray? and SpikeSourcePoisson? in brian. Also simplify the weights conversion by just defining the same convention as in nest : all inhibitory target should now have negative values

Files:

• trunk/src/brian/__init__.py (modified) (10 diffs)
• trunk/src/brian/cells.py (modified) (2 diffs)
• trunk/src/brian/connectors.py (modified) (2 diffs)

trunk/src/brian/__init__.py

@@ -20 +20 @@
-DEFAULT_BUFFER_SIZE = 10000
-
+class MultipleSpikeGeneratorGroupWithDelays(brian.MultipleSpikeGeneratorGroup):
+   def __init__(self,spiketimes,clock=None,max_delay=0):
+       clock = brian.guess_clock(clock)
+       thresh = brian.directcontrol.MultipleSpikeGeneratorThreshold(spiketimes)
+       brian.NeuronGroup.__init__(self,len(spiketimes),model=brian.LazyStateUpdater(),threshold=thresh,clock=clock,max_delay=max_delay)
+       
+
+class PoissonGroupWithDelays(brian.NeuronGroup):
+    def __init__(self,N,rates=0,clock=None,max_delay=0):
+        brian.NeuronGroup.__init__(self,N,model=brian.LazyStateUpdater(),threshold=brian.PoissonThreshold(),clock=clock,max_delay=max_delay)
+        if callable(rates): # a function is passed
+            self._variable_rate=True
+            self.rates=rates
+            self._S0[0]=self.rates(self.clock.t)
+        else:
+            self._variable_rate=False
+            self._S[0,:]=rates
+            self._S0[0]=rates
+        self.var_index={'rate':0}
+
-# ==============================================================================
-#   Utility classes and functions
@@ -39 +59 @@
-    def __getattr__(self, name):
-        try:
-brian.MultipleSpikeGeneratorGroup
+MultipleSpikeGeneratorGroupWithDelays
-                if name == "spike_times":
-                    return 1000*numpy.array(self.parent.brian_cells._threshold.spiketimes[int(self)])
@@ -50 +70 @@
-    def set_native_parameters(self, parameters):
-        for key, value in parameters.items():
-brian.MultipleSpikeGeneratorGroup
+MultipleSpikeGeneratorGroupWithDelays
-                if key == "spike_times":
-                    spike_times = 0.001*numpy.array(value)
@@ -128 +148 @@
-    global simclock
-    return simclock.t
+
+def get_net_status():
+    global net
+    return net
-
-def num_processes():
@@ -251 +275 @@
-                rate              = self.cellparams['rate']
-                fct               = self.celltype.fct
-
-
+
-            elif isinstance(self.celltype, SpikeSourceArray):
-                spike_times = 0.001*numpy.array(self.cellparams['spike_times'])
-
-
+
-            else:
-                v_thresh   = self.cellparams['v_thresh']
@@ -483 +505 @@
-        - or a list containing the ids of the cells to record.
-        """
-
+, simclock
-        if record_from:
-            if isinstance(record_from,int):
@@ -490 +512 @@
-        else:
-            record_from = True
-
+, clock=simclock
-        net.add(self.vm_recorder)
-    
@@ -501 +523 @@
-        - or a list containing the ids of the cells to record.
-        """
-
+, simclock
-        if record_from:
-            if isinstance(record_from,int):
@@ -508 +530 @@
-        else:
-            record_from = True
-
-
+, clock=simclock
+, clock=simclock
-        net.add(self.ce_recorder)
-        net.add(self.ci_recorder)
@@ -557 +579 @@
-        Useful for small populations, for example for single neuron Monte-Carlo.
-        """
-
+
+
+
+
+
+
-
-    def meanSpikeCount(self, gather=True):

trunk/src/brian/cells.py

@@ -89 +89 @@
-    )
-    eqs= brian.Equations('''
-+
+-
-        dge/dt = (2.7182818284590451*ye-ge)/tau_syn_E  : 1 
-        dye/dt = -ye/tau_syn_E                         : 1
@@ -124 +124 @@
-    )
-    eqs= brian.Equations('''
-+
+-
-        dge/dt = -ge/tau_syn_E : 1
-        dgi/dt = -gi/tau_syn_I : 1

trunk/src/brian/connectors.py

@@ -5 +5 @@
-
-from pyNN import common
-
+, PoissonGroupWithDelays
-import brian_no_units_no_warnings
-import brian, types
@@ -22 +22 @@
-    else:
-        target=projection.post.celltype.synapses['inh']
-
+
+
+
+
+
-
-def _convertWeight(weight, projection):
-brian.PoissonGroup
-projection.pre.brian_cells.rate[0]
+PoissonGroupWithDelays
+10
-    if isinstance(weight, numpy.ndarray):
-        all_negative = (weight<=0).all()
-        all_positive = (weight>=0).all()
-        assert all_negative or all_positive, "Weights must be either all positive or all negative"
-
-
-
-
-
-
+
+
-    elif is_number(weight):
-
-
-
-
-
-
+
+
+
+
-    return weight
-