Adding input type <spikeGeneratorRefPoisson>

Author: pgleeson

LEMSexamples/LEMS_NML2_Ex16_Inputs.xml

@@ -29,17 +29,19 @@
 <Include file="../examples/NML2_Inputs.nml"/>
 
 <network id="net1">
-    <population id="izhPop" component="RS" size="12"/>
+    <population id="izhPop" component="RS" size="13"/>
 
     <population id="spikeArrPop" component="spkArr" size="1"/>
     <population id="spikeGenRegularPop" component="spikeGenRegular" size="1"/>
     <population id="spikeGenPoissonPop" component="spikeGenPoisson" size="1"/>
+    <population id="spikeGenRefPoissonPop" component="spikeGenRefPoisson" size="1"/>
     <population id="spikeGenRandomPop" component="spikeGenRandom" size="1"/>
 
     <explicitInput target="izhPop[0]" input="pulseGen0" destination="synapses"/>
     <explicitInput target="izhPop[1]" input="sg0" destination="synapses"/>
     <explicitInput target="izhPop[2]" input="rg0" destination="synapses"/>
     <explicitInput target="izhPop[3]" input="vClamp0" destination="synapses"/>
+    
     <explicitInput target="izhPop[8]" input="poissonFiringSyn" destination="synapses"/>
     <explicitInput target="izhPop[9]" input="ci0" destination="synapses"/>
     <explicitInput target="izhPop[10]" input="transPoissonFiringSyn" destination="synapses"/>
@@ -49,6 +51,7 @@
     <synapticConnection from="spikeGenRegularPop[0]" to="izhPop[5]" synapse="syn1" destination="synapses"/>
     <synapticConnection from="spikeGenRandomPop[0]" to="izhPop[6]" synapse="syn1" destination="synapses"/>
     <synapticConnection from="spikeGenPoissonPop[0]" to="izhPop[7]" synapse="syn1" destination="synapses"/>
+    <synapticConnection from="spikeGenRefPoissonPop[0]" to="izhPop[12]" synapse="syn1" destination="synapses"/>
 </network>
 
         <!-- End of NeuroML2 content -->
@@ -82,9 +85,12 @@
     </Display>
 
     <Display id="d40" title="Ex16: Izhikevich cell, spiking inputs, time since spikes" timeScale="1ms" xmin="-20" xmax="320" ymin="-5" ymax="45">
-        <Line id ="Regular spike gen t since" quantity="spikeGenRegularPop[0]/tsince" scale="1ms"  color="#3fffaa" timeScale="1ms"/>
-        <Line id ="Poisson spike gen t since" quantity="spikeGenRandomPop[0]/tsince" scale="1ms"  color="#3ff9999" timeScale="1ms"/>
-        <Line id ="Spike array t since" quantity="spikeArrPop[0]/tsince" scale="1ms"  color="#3faa99" timeScale="1ms"/>
+        <Line id ="regular spike gen t since" quantity="spikeGenRegularPop[0]/tsince" scale="1ms"  color="#3fffaa" timeScale="1ms"/>
+        <Line id ="poisson spike gen t since" quantity="spikeGenPoissonPop[0]/tsince" scale="1ms"  color="#3ff9999" timeScale="1ms"/>
+        <Line id ="poisson ref. spike gen t since" quantity="spikeGenRefPoissonPop[0]/tsince" scale="1ms"  color="#3ff1119" timeScale="1ms"/>
+        <Line id ="random spike t since" quantity="spikeGenRandomPop[0]/tsince" scale="1ms"  color="#aaf9999" timeScale="1ms"/>
+        
+        <Line id ="spike array t since" quantity="spikeArrPop[0]/tsince" scale="1ms"  color="#3faa99" timeScale="1ms"/>
         <Line id ="Transient poisson spike gen" quantity="izhPop[10]/transPoissonFiringSyn/tsince" scale="1ms"  color="#000000" timeScale="1ms"/>
     </Display>
 
@@ -97,6 +103,8 @@
 	    color="#01A9DB" timeScale="1ms"/>
       <Line id="poisson spike gen" quantity="izhPop[7]/v" scale="1mV"
 	    color="#8000FF" timeScale="1ms"/>
+      <Line id="poisson ref. spike gen" quantity="izhPop[12]/v" scale="1mV"
+	    color="#80aaaF" timeScale="1ms"/>
       <Line id="transient poisson spike gen" quantity="izhPop[10]/v" scale="1mV"
 	    color="#ff00FF" timeScale="1ms"/>
     </Display>

LEMSexamples/test/.test.ex16.jnml.omt

@@ -25,7 +25,7 @@ experiments:
         spike detection: 
           method: threshold
           threshold: -58.6
-        tolerance:  0.00002
+        tolerance:  1.8691938167e-05
   compound:
     observables:
       spike times:

NeuroML2CoreTypes/Inputs.xml

@@ -151,6 +151,29 @@
         </Dynamics>
     </ComponentType>
 
+    
+    <ComponentType name="spikeGeneratorRefPoisson"
+                 extends="spikeGeneratorPoisson"
+                 description="Generator of spikes whose ISI distribution is the maximum entropy distribution over [_minimumISI, +infinity) with mean 1/_averageRate">
+        <Parameter name="minimumISI" dimension="time"/>
+        <Dynamics>
+            <StateVariable name="tsince" dimension="time" exposure="tsince"/>
+            <StateVariable name="isi" dimension="time"/>
+            <TimeDerivative variable="tsince" value="1"/>
+
+            <OnStart>
+                <StateAssignment variable="tsince" value="0"/>
+                <StateAssignment variable="isi" value="minimumISI - (averageIsi-minimumISI) * log(1 - random(1))"/>
+            </OnStart>
+
+            <OnCondition test="tsince .gt. isi">
+                <StateAssignment variable="tsince" value="0"/>
+                <StateAssignment variable="isi" value="minimumISI - (averageIsi-minimumISI) * log(1 - random(1))"/>
+                <EventOut port="spike"/>
+            </OnCondition>
+        </Dynamics>
+    </ComponentType>
+    
 
     <ComponentType name="poissonFiringSynapse"
                    description="Poisson spike generator connected to single synapse providing an input current"

Schemas/NeuroML2/NeuroML_v2beta5.xsd

@@ -588,6 +588,8 @@
                     minOccurs="0" maxOccurs="unbounded"/>
             <xs:element name="spikeGeneratorPoisson" type="SpikeGeneratorPoisson"
                     minOccurs="0" maxOccurs="unbounded"/>
+            <xs:element name="spikeGeneratorRefPoisson" type="SpikeGeneratorRefPoisson"
+                    minOccurs="0" maxOccurs="unbounded"/>
             <xs:element name="poissonFiringSynapse" type="PoissonFiringSynapse"
                     minOccurs="0" maxOccurs="unbounded"/>
             <xs:element name="transientPoissonFiringSynapse" type="TransientPoissonFiringSynapse"
@@ -2460,6 +2462,15 @@
         </xs:complexContent>
     </xs:complexType>
 
+    <xs:complexType name="SpikeGeneratorRefPoisson">
+        <xs:complexContent>
+            <xs:extension base="SpikeGeneratorPoisson">
+                <xs:attribute name="minimumISI" type="Nml2Quantity_time"
+                              use="required"/>
+            </xs:extension>
+        </xs:complexContent>
+    </xs:complexType>
+
     <xs:complexType name="PoissonFiringSynapse">
         <xs:complexContent>
             <xs:extension base="Standalone">

examples/NML2_Inputs.nml

@@ -64,6 +64,8 @@
                   maxISI="30 ms"/>
 
     <spikeGeneratorPoisson id="spikeGenPoisson" averageRate="50 Hz"/>
+    
+    <spikeGeneratorRefPoisson id="spikeGenRefPoisson" averageRate="50 Hz" minimumISI="10 ms"/>
 
     <poissonFiringSynapse id="poissonFiringSyn" averageRate="10 Hz" synapse="synInput" spikeTarget="./synInput"/>