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bsumirakbsumirak
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adjusted to recent UG changes concerning synapse types, synapse handler and distributor
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9 files changed

+418
-397
lines changed

9 files changed

+418
-397
lines changed

‎src/main/java/edu/gcsc/vrl/neurobox/NeuroBoxPluginConfigurator.java

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@@ -155,7 +155,7 @@ public void register(PluginAPI api)
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vapi.addComponent(Hodgkin_Huxley.class);
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vapi.addComponent(Hodgkin_Huxley_Nernst.class);
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vapi.addComponent(Leakage.class);
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vapi.addComponent(SynapseHandler.class);
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vapi.addComponent(SynapseHandler_VRL.class);
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// membrane potential mapping
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vapi.addComponent(MembranePotentialMapping.class);

‎src/main/java/edu/gcsc/vrl/neurobox/SynapseDistributionGenerator.java

Lines changed: 257 additions & 130 deletions
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‎src/main/java/edu/gcsc/vrl/neurobox/SynapseHandler.java

Lines changed: 0 additions & 234 deletions
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‎src/main/java/edu/gcsc/vrl/neurobox/SynapseHandler_VRL.java

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@@ -0,0 +1,147 @@
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package edu.gcsc.vrl.neurobox;
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import edu.gcsc.vrl.ug.api.I_SynapseHandler;
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import edu.gcsc.vrl.ug.api.SynapseHandler;
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import eu.mihosoft.vrl.annotation.ComponentInfo;
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import eu.mihosoft.vrl.annotation.MethodInfo;
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import eu.mihosoft.vrl.annotation.ParamInfo;
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import java.io.Serializable;
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/**
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*
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* @author mbreit
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* @date 22-06-2015
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*/
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@ComponentInfo(name="Synapse Handler", category="Neuro/cable")
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public class SynapseHandler_VRL implements Serializable
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{
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private static final long serialVersionUID = 1L;
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private transient I_SynapseHandler synHandler = null;
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/**
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* @return Hodgkin-Huxley channel object
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*/
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@MethodInfo(name="create synapse handler", valueName="synapse handler", initializer=true, hide=false, interactive=false)
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public I_SynapseHandler create()
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{
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// construct new synapse handler object
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synHandler = new SynapseHandler();
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return synHandler;
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}
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@MethodInfo(name="set ALPHA synapse activation timing", interactive=false)
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public void set_alpha_synapse_activation_timing
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(
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/// start time
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@ParamInfo(name="mean onset [s]",
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style="default",
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options="value=0.01; description=\"default: 10 ms\"")
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Double onset,
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/// duration
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@ParamInfo(name="mean tau [s]",
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style="default",
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options="value=2e-3; description=\"default: 2 ms\"")
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Double tau,
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/// peak conductance
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@ParamInfo(name="mean peak conductance [S]",
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style="default",
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options="value=1.2e-9; description=\"default: 1.2 nS\"")
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Double peak_cond,
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/// std deviation of start time
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@ParamInfo(name="std deviation onset [s]",
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style="default",
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options="value=0.003; description=\"default: 3 ms\"")
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Double onset_dev,
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/// std deviation of duration
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@ParamInfo(name="std deviation tau [s]",
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style="default",
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options="value=2e-4; description=\"default: 200 us\"")
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Double tau_dev,
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/// std deviation of peak conductance
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@ParamInfo(name="std deviation peak conductance [S]",
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style="default",
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options="value=1e-10; description=\"default: 100 pS\"")
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Double peak_cond_dev
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)
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{
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check_syn_handler();
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synHandler.set_activation_timing_alpha(onset, tau, peak_cond, onset_dev, tau_dev, peak_cond_dev, true);
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}
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@MethodInfo(name="set EXP2 synapse activation timing", interactive=false)
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public void set_exp2_synapse_activation_timing
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(
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/// average start time
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@ParamInfo(name="mean onset [s]",
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style="default",
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options="value=0.01; description=\"default: 10 ms\"")
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Double onset_mean,
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/// tau1
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@ParamInfo(name="mean tau1 [s]",
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style="default",
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options="value=7e-4; description=\"0.7-1 ms for AMPA\"")
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Double tau1_mean,
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/// tau2
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@ParamInfo(name="mean tau2 [s]",
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style="default",
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options="value=5e-3; description=\"5-8 ms for AMPA\"")
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Double tau2_mean,
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/// peak conductance
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@ParamInfo(name="mean peak conductance [S]",
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style="default",
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options="value=1.2e-9; description=\"default: 1.2 nS\"")
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Double peak_cond_mean,
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/// std deviation of start time
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@ParamInfo(name="std deviation onset [s]",
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style="default",
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options="value=3e-3; description=\"default: 3 ms\"")
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Double onset_dev,
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/// std deviation of tau1
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@ParamInfo(name="std deviation tau1 [s]",
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style="default",
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options="value=0.0; description=\"default 0\"")
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Double tau1_dev,
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/// std deviation of tau2
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@ParamInfo(name="std deviation tau2 [s]",
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style="default",
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options="value=0.0; description=\"default 0\"")
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Double tau2_dev,
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/// std deviation of peak conductance
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@ParamInfo(name="std deviation peak conductance [S]",
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style="default",
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options="value=1e-10; description=\"default: 100 pS\"")
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Double peak_cond_dev
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)
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{
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check_syn_handler();
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synHandler.set_activation_timing_biexp(onset_mean, tau1_mean, tau2_mean, peak_cond_mean, onset_dev, tau1_dev, tau2_dev, peak_cond_dev, true);
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}
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@MethodInfo(noGUI=true)
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private void check_syn_handler()
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{
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if (synHandler == null)
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{
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eu.mihosoft.vrl.system.VMessage.exception("Usage before initialization: ",
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"No method can be called on synapse handler object before it has been initialized"
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+ "using the 'create()' method.");
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}
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}
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}

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