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Anonymous committed f0ec615

Added `Section.record_spikes()` and `Mechanism.insert_into()`

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+
+
+Version 2.0 dated 2006-09-05.
     >>> leak = Mechanism('pas', {'e': -65, 'g': 0.0002})
     >>> hh = Mechanism('hh')
     """
-    def __init__(self, name, parameters={}):
+    def __init__(self, name, **parameters):
         self.name = name
         self.parameters = parameters
 
+    def insert_into(self, section):
+        section.insert(mechanism.name)
+        for name, value in self.parameters.items():
+            for segment in section:
+                mech = getattr(segment, mechanism.name)
+                setattr(mech, name, value)
+
 
 class Section(nrn.Section):
     """
             self.connect(parent, connect_to, 0)
         # add ion channels
         for mechanism in mechanisms:
-            self.insert(mechanism.name)
-            for name, value in mechanism.parameters.items():
-                for segment in self:
-                    mech = getattr(segment, mechanism.name)
-                    setattr(mech, name, value)
-        self.synapses = []
+            mechanism.insert_into(self)
+        #self.synapses = {}
 
-    def add_synapse(self, type, parameters={}, location=0.5):
+    def add_synapse(self, label, type, location=0.5, **parameters):
         synapse = getattr(h, type)(location, sec=self)
         for name, value in parameters.items():
             setattr(synapse, name, value)
-        self.synapses.append(synapse)
+        if hasattr(self, label):
+            raise Exception("Can't overwrite synapse labels (to keep things simple)")
+        setattr(self, label, synapse)
         
-    def plot(self, variable, location=0.5):
+    def plot(self, variable, location=0.5, tmin=0, tmax=5, xmin=-80, xmax=40):
         import neuron.gui
         self.graph = h.Graph()
         h.graphList[0].append(self.graph)
-        self.graph.size(0, 5, -80, 40)
+        self.graph.size(tmin, tmax, xmin, xmax)
         self.graph.addvar('%s(%g)' % (variable, location), sec=self)
 
+    def record_spikes(self, threshold=-30):
+        self.spiketimes = h.Vector()
+        self.spikecount = h.APCount(0.5, sec=self)
+        self.spikecount.thresh = threshold
+        self.spikecount.record(self.spiketimes)
+        
 
 if __name__ == "__main__":
     
     py_modules=['nrnutils'],
     author = "Andrew P. Davison",
     author_email = "andrewpdavison@gmail.com",
-    description = "",
+    description = "Some tools for use with the NEURON simulator (http://www.neuron.yale.edu/neuron/)",
     license = "CeCILL http://www.cecill.info",
     keywords = "computational science neuroscience simulation",
     url = "https://bitbucket.org/apdavison/nrnutils",