Synapses on improvments complete

JaneliaSciComp · Oct 21, 2015 · 46fec2a · 46fec2a
1 parent 8c03d66
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Showing 3 changed files with 36 additions and 24 deletions.
diff --git a/Source/Scripts/Synapses.py b/Source/Scripts/Synapses.py
@@ -10,25 +10,30 @@
 regionA = network.createRegion(name = 'A')
 regionB = network.createRegion(name = 'B')
 
-neuron1 = network.createNeuron(name = '1', neurotransmitters = [library.neurotransmitter('GABA')], functions = [Neuron.Function.SENSORY])
+neuron1 = network.createNeuron(name = '1', neurotransmitters = [library.neurotransmitter('GABA')], functions = [Neuron.Function.SENSORY], activation = 'excitatory')
 neuron1.arborize(regionA, True, False)
 neuron1.arborize(regionB, True, False)
 
 neuron2 = network.createNeuron(name = '2', functions = [Neuron.Function.SENSORY])
 neuron2.arborize(regionA, True, False)
 neuron2.arborize(regionB, True, False)
 
-neuron1.synapseOn(neuron2)
+neuron1.synapseOn(neuron2, preSynapticRegion=regionA, postSynapticRegion=regionB)
+
 neuron2.synapseOn(neuron1)
 
 neuron3 = network.createNeuron(name = '3', functions = [Neuron.Function.INTERNEURON])
 neuron3.arborize(regionA)
 neuron3.arborize(regionB)
 
+neuron1.synapseOn(neuron3)
+
 neuron4 = network.createNeuron(name = '4', neurotransmitters = [library.neurotransmitter('ACh')], functions = [Neuron.Function.MOTOR])
 neuron4.arborize(regionA, False, True)
 neuron4.arborize(regionB, False, True)
 
+neuron1.synapseOn(neuron4)
+
 neuron5 = network.createNeuron(name = '5', neurotransmitters = [library.neurotransmitter('ACh')], functions = [Neuron.Function.MOTOR])
 neuron5.arborize(regionA, False, True)
 neuron5.arborize(regionB, False, True)

diff --git a/Source/network/neuron.py b/Source/network/neuron.py
@@ -459,44 +459,51 @@ def searchPost(self, preRegion = None, postRegion = None, postNeuron = None, act
         """
         Searches for post-synaptic sites
         """
-        from re import search
         # limit synapse to where neuron is presynaptic
-        synapses = [connection for connection in self.connections() if isinstance(connection, Synapse) and connection.preSynapticNeuron() == self]
-        if preRegion:
-            synapses = [synapse for synapse in synapses if search(preRegion, synapse.preSynapticRegion)]
-        if postRegion:
-            synapses = [synapse for synapse in synapses if search(postRegion, synapse.postSynapticRegion)]
-        if activation:
-            synapses = [synapse for synapse in synapses if synapse.activation == activation]
+        synapses = [connection for connection in self.synapses() if connection.preSynapticNeuron() == self]
+        synapses = self._filterSynapsesForSearch(synapses, preRegion = preRegion, postRegion = postRegion, activation = activation)
         # get post synaptic neurons
         neurons = []
         for synapse in synapses:
             neurons.extend(synapse.postSynapticNeurons())
-        if neurotransmitter:
-            neurons = [neuron for neuron in neurons if neurotransmitter in neuron.neurotransmitters]
+        neurons = self._filterNeuronsForSearch(neurons, neurotransmitter=neurotransmitter, name=postNeuron)
         return neurons
 
     def searchPre(self, preRegion = None, postRegion = None, preNeuron = None, activation = None, neurotransmitter = None):
         """
         Searches for pre-synaptic sites
         """
         # limit synapse to where neuron is postsynaptic
-        synapses = [connection for connection in self.connections() if isinstance(connection, Synapse) and self in connection.postSynapticNeurons()]
-        # Filter synapses 
-        if preRegion:
-            synapses = [synapse for synapse in synapses if search(preRegion, synapse.preSynapticRegion)]
-        if postRegion:
-            synapses = [synapse for synapse in synapses if search(postRegion, synapse.postSynapticRegion)]
-        if activation:
-            synapses = [synapse for synapse in synapses if synapse.activation == activation]
+        synapses = [connection for connection in self.synapses() if self in connection.postSynapticNeurons()]
+        synapses = self._filterSynapsesForSearch(synapses, preRegion = preRegion, postRegion = postRegion, activation = activation)
         # get pre synaptic neurons
         neurons = []
         for synapse in synapses:
             neurons.append(synapse.preSynapticNeuron())
+        neurons = self._filterNeuronsForSearch(neurons, neurotransmitter = neurotransmitter, name = preNeuron)
+        return neurons
+
+
+    def _filterNeuronsForSearch(self, neurons, neurotransmitter = None, name = None):
+        from re import search
         if neurotransmitter:
             neurons = [neuron for neuron in neurons if neurotransmitter in neuron.neurotransmitters]
+        if name:
+            neurons = [neuron for neuron in neurons if search(name, neuron.name)]
         return neurons
-
+
+
+    def _filterSynapsesForSearch(self, synapses, preRegion = None, postRegion = None, activation = None):
+        from re import search
+        if preRegion:
+            synapses = [synapse for synapse in synapses if synapse.preSynapticRegion and search(preRegion, synapse.preSynapticRegion.name)]
+        if postRegion:
+            synapses = [synapse for synapse in synapses if synapse.postSynapticRegion and search(postRegion, synapse.postSynapticRegion.name)]
+        if activation:
+            synapses = [synapse for synapse in synapses if synapse.activation and synapse.activation == activation]
+        return synapses
+
+
     @classmethod
     def _defaultVisualizationParams(cls):
         params = NeuroObject._defaultVisualizationParams()

diff --git a/Source/network/synapse.py b/Source/network/synapse.py
@@ -13,7 +13,7 @@
 
 
 class Synapse(NeuroObject):
-    def __init__(self, network, preSynapticNeurite = None, postSynapticPartners = [], activation = None, presynapticRegion = None, postsynapticRegion = None, *args, **keywords):
+    def __init__(self, network, preSynapticNeurite = None, postSynapticPartners = [], activation = None, preSynapticRegion = None, postSynapticRegion = None, *args, **keywords):
         """
         A Synapse object represents a chemical synapse between a single pre-synaptic neurite and one or more post-synaptic neurites.
         
@@ -28,8 +28,8 @@ def __init__(self, network, preSynapticNeurite = None, postSynapticPartners = []
         self.preSynapticNeurite = preSynapticNeurite
         self.postSynapticPartners = postSynapticPartners
         self.activation = activation
-        self.preSynapticRegion = presynapticRegion
-        self.postSynapticRegion = postsynapticRegion
+        self.preSynapticRegion = preSynapticRegion
+        self.postSynapticRegion = postSynapticRegion
 
 
     def defaultName(self):