- safeD(double) - Method in class cnslab.cnsnetwork.VSICLIFNeuron
-
absolute time t
- safeD(double) - Method in class cnslab.cnsnetwork.VSICLIFNeuronV2
-
Safe derivative, good for Newton method, see D'hane paper
- safeDerivative(double) - Method in class cnslab.cnsnetwork.MiNiNeuron
-
Computes the "safe derivative" (see D'Haene, 2009) of the
thresholdDiff function.
- safeRootFind(Polynomial, double, double) - Method in class cnslab.cnsmath.Polynomial
-
- safeRootFind(double[], double, double) - Static method in class cnslab.cnsnetwork.FunUtil
-
Deprecated.
- saveBitmap(String, int[], int, int) - Method in class cnslab.image.BMPFile
-
- saveImage(int[][][], String) - Static method in class cnslab.image.imageIO
-
- saveInt - Variable in class cnslab.cnsnetwork.FitFun
-
Deprecated.
- scaffold - Variable in class cnslab.cnsnetwork.LayerStructure
-
Scaffold is used to help to build up the network structure,
which should be private
- scale(double) - Method in class cnslab.cnsmath.Polynomial
-
- scale(double[], double) - Static method in class cnslab.cnsnetwork.FunUtil
-
Deprecated.
- sd(double[]) - Static method in class cnslab.cnsnetwork.FunUtil
-
Compute the standard deviation of the vector
- sd(int, double[]) - Static method in class cnslab.cnsnetwork.FunUtil
-
Compute the standard deviation of the vector, starting at start
- sd(int, int, double[]) - Static method in class cnslab.cnsnetwork.FunUtil
-
- secondItem() - Method in class cnslab.cnsnetwork.TreeQueue
-
Second item from the queue
- sectionsInAxisX - Static variable in class cnslab.cnsnetwork.LayerStructure
-
- sectionsInAxisY - Static variable in class cnslab.cnsnetwork.LayerStructure
-
- Seed - Class in cnslab.cnsmath
-
- Seed(int) - Constructor for class cnslab.cnsmath.Seed
-
- seed - Variable in class cnslab.cnsmath.Seed
-
- seed - Variable in class cnslab.cnsnetwork.Network
-
the seed value for this network
- seed - Variable in class cnslab.cnsnetwork.Stimulus
-
- seedInt - Variable in class cnslab.cnsnetwork.FitFun
-
Deprecated.
- seedInt - Variable in class cnslab.cnsnetwork.MainSimulator
-
Seed integer provided by user
- seedInt - Variable in class edu.jhu.mb.ernst.net.PeerInfo
-
- send(jpvmSendConnection) - Method in class jpvm.jpvmBuffer
-
- send(jpvmSendConnection) - Method in class jpvm.jpvmMessage
-
- send(DataOutputStream) - Method in class jpvm.jpvmTaskId
-
- sendNeurons - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- sendSeed - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- sendSpike - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- sendTick - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- sendTids - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- sendTids2 - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- sendTime - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- Seq<E> - Interface in edu.jhu.mb.ernst.util.seq
-
Read-only access to a sequence such as an Object array or a List.
- setBlack() - Method in class cnslab.cnsmath.RBTNode
-
Sets the color of the node to black.
- setCount(int) - Method in class cnslab.cnsmath.RBTree
-
set the element count and update version_ if changed
- setLayerNeurons(Layer, int) - Method in class cnslab.cnsnetwork.Recorder
-
Set the layer of neurons which needs to be recorded.
- setLayerNeurons(Layer) - Method in class cnslab.cnsnetwork.Recorder
-
Set the layer of neurons which needs to be recorded.
- setLetGo() - Method in class cnslab.cnsnetwork.PMainBK
-
Deprecated.
set a new value to letGo
- setLocalTime(double, int) - Method in class cnslab.cnsnetwork.Network
-
set a new value to localTime
- setMemV(double) - Method in class cnslab.cnsnetwork.MiNiNeuron
-
set the membrane voltage
- setMemV(double) - Method in class cnslab.cnsnetwork.SIFNeuron
-
set a new value to memV
- setMemV(double) - Method in class cnslab.cnsnetwork.VSICLIFNeuron
-
- setMemV(double) - Method in class cnslab.cnsnetwork.VSICLIFNeuronV2
-
set the membrane voltage
- setModulationFactor(String, Double) - Method in interface edu.jhu.mb.ernst.model.ModulatedSynapse
-
The modulation factor is applied immediately to the weight.
- setModulationFactor(String, Double) - Method in class edu.jhu.mb.ernst.model.synapse.ModulatedSynapseImp
-
- setMultiplierX(int) - Method in class cnslab.cnsnetwork.Layer
-
- setMultiplierY(int) - Method in class cnslab.cnsnetwork.Layer
-
- setNeuronType(String) - Method in class cnslab.cnsnetwork.Layer
-
- setPrefix(String) - Method in class cnslab.cnsnetwork.Layer
-
- setRecord(boolean) - Method in class cnslab.cnsnetwork.BKPoissonNeuron
-
- setRecord(boolean) - Method in class cnslab.cnsnetwork.MiNiNeuron
-
- setRecord(boolean) - Method in interface cnslab.cnsnetwork.Neuron
-
set the neuron record or not.
- setRecord(boolean) - Method in class cnslab.cnsnetwork.SIFNeuron
-
set the neuron record or not.
- setRecord(boolean) - Method in class cnslab.cnsnetwork.SYNNeuron
-
set the neuron record or not.
- setRecord(boolean) - Method in class cnslab.cnsnetwork.UserSenNeuron
-
- setRecord(boolean) - Method in class cnslab.cnsnetwork.VSICLIFNeuron
-
- setRecord(boolean) - Method in class cnslab.cnsnetwork.VSICLIFNeuronV2
-
- setRed() - Method in class cnslab.cnsmath.RBTNode
-
Sets the color of the node to red.
- setSeed(Seed) - Method in class cnslab.cnsnetwork.LayerStructure
-
- setSuffix(String) - Method in class cnslab.cnsnetwork.Layer
-
- setTargetNeuronIndex(int) - Method in interface edu.jhu.mb.ernst.model.MutableSynapse
-
- setTargetNeuronIndex(int) - Method in class edu.jhu.mb.ernst.model.synapse.MutableSynapseImp
-
- setTHost(long) - Method in class cnslab.cnsnetwork.BKPoissonNeuron
-
- setTHost(long) - Method in class cnslab.cnsnetwork.MiNiNeuron
-
- setTHost(long) - Method in interface cnslab.cnsnetwork.Neuron
-
set the target host id, 0 means none, 1 means yes
- setTHost(long) - Method in class cnslab.cnsnetwork.SIFNeuron
-
set the target host id //0 means none , 1 means yes
- setTHost(long) - Method in class cnslab.cnsnetwork.SYNNeuron
-
set the target host id //0 means none , 1 means yes
- setTHost(long) - Method in class cnslab.cnsnetwork.UserSenNeuron
-
- setTHost(long) - Method in class cnslab.cnsnetwork.VSICLIFNeuron
-
- setTHost(long) - Method in class cnslab.cnsnetwork.VSICLIFNeuronV2
-
- setTimeOfLastUpdate(double) - Method in class cnslab.cnsnetwork.MiNiNeuron
-
- setTimeOfLastUpdate(double) - Method in class cnslab.cnsnetwork.SIFNeuron
-
set a new value to timeOfLastUpdate
- setTimeOfLastUpdate(double) - Method in class cnslab.cnsnetwork.VSICLIFNeuron
-
- setTimeOfLastUpdate(double) - Method in class cnslab.cnsnetwork.VSICLIFNeuronV2
-
- setTimeOfNextFire(double) - Method in class cnslab.cnsnetwork.BKPoissonNeuron
-
- setTimeOfNextFire(double) - Method in class cnslab.cnsnetwork.MiNiNeuron
-
- setTimeOfNextFire(double) - Method in interface cnslab.cnsnetwork.Neuron
-
set a new value to timeOfNextFire
- setTimeOfNextFire(double) - Method in class cnslab.cnsnetwork.SIFNeuron
-
set a new value to timeOfNextFire
- setTimeOfNextFire(double) - Method in class cnslab.cnsnetwork.SYNNeuron
-
- setTimeOfNextFire(double) - Method in class cnslab.cnsnetwork.UserSenNeuron
-
- setTimeOfNextFire(double) - Method in class cnslab.cnsnetwork.VSICLIFNeuron
-
- setTimeOfNextFire(double) - Method in class cnslab.cnsnetwork.VSICLIFNeuronV2
-
- setType(byte) - Method in interface edu.jhu.mb.ernst.model.MutableSynapse
-
- setType(byte) - Method in class edu.jhu.mb.ernst.model.synapse.MutableSynapseImp
-
- setWeight(float) - Method in interface edu.jhu.mb.ernst.model.MutableSynapse
-
- setWeight(float) - Method in class edu.jhu.mb.ernst.model.synapse.MutableSynapseImp
-
- show(PrintStream) - Method in class cnslab.cnsnetwork.FiboQueue
-
show all the elements in the Queue in order
- show() - Method in class cnslab.cnsnetwork.FiboQueue
-
- show(PrintStream) - Method in class cnslab.cnsnetwork.MTreeQueue
-
- show() - Method in class cnslab.cnsnetwork.MTreeQueue
-
- show - Variable in class cnslab.cnsnetwork.PlotResult
-
- show(PrintStream) - Method in class cnslab.cnsnetwork.PriQueue
-
show all the elements in the Queue in order
- show() - Method in class cnslab.cnsnetwork.PriQueue
-
- show(PrintStream) - Method in interface cnslab.cnsnetwork.Queue
-
Print out the queue element to the PrintStream p
- show() - Method in interface cnslab.cnsnetwork.Queue
-
Print out the queue element to the standard output
- show(PrintStream) - Method in class cnslab.cnsnetwork.TreeQueue
-
show all the elements in the Queue in order
- show() - Method in class cnslab.cnsnetwork.TreeQueue
-
Print out the queue element to the standard output
- showPic(Object) - Method in class cnslab.gui.mainErnst
-
- showXMLFile() - Method in class cnslab.gui.mainErnst
-
- SIFNeuron - Class in cnslab.cnsnetwork
-
Implemented simple integrate and fire neuron.
- SIFNeuron(SIFNeuronPara) - Constructor for class cnslab.cnsnetwork.SIFNeuron
-
- SIFNeuronPara - Class in cnslab.cnsnetwork
-
The data structure to store parameters of the SIF neuron.
- SIFNeuronPara() - Constructor for class cnslab.cnsnetwork.SIFNeuronPara
-
- SimpleErrorHandler - Class in cnslab.cnsnetwork
-
- SimpleErrorHandler() - Constructor for class cnslab.cnsnetwork.SimpleErrorHandler
-
- simulatorParser - Variable in class cnslab.cnsnetwork.Network
-
the system background firing rates
- simulatorParser - Variable in class cnslab.cnsnetwork.Recorder
-
- SimulatorParser - Class in cnslab.cnsnetwork
-
Simulator Parser, to parse XML file
- SimulatorParser(Seed, File) - Constructor for class cnslab.cnsnetwork.SimulatorParser
-
- SimulatorParser(Seed, Document) - Constructor for class cnslab.cnsnetwork.SimulatorParser
-
- SimulatorParser() - Constructor for class cnslab.cnsnetwork.SimulatorParser
-
- simulatorParser - Variable in class cnslab.cnsnetwork.Stimulus
-
- singleUnit - Variable in class cnslab.cnsnetwork.Recorder
-
Single unit array, stored the array of recorded index of neurons
- size() - Method in class cnslab.cnsmath.RBCell
-
Return the number of nodes in the subtree
- size - Variable in class cnslab.cnsnetwork.SizeID
-
- size() - Method in class edu.jhu.mb.ernst.util.seq.ListSeq
-
- size() - Method in interface edu.jhu.mb.ernst.util.seq.Seq
-
- SizeID - Class in cnslab.cnsnetwork
-
- SizeID(int, int) - Constructor for class cnslab.cnsnetwork.SizeID
-
- Slot<E> - Interface in edu.jhu.mb.ernst.util.slot
-
Mail slot for receiving messages to be processed, stored, or relayed.
- smallestRoot() - Method in class cnslab.cnsmath.Polynomial
-
- smallestRoot(double[]) - Static method in class cnslab.cnsnetwork.FunUtil
-
Deprecated.
- sortSynapses(int) - Method in class cnslab.cnsnetwork.LayerStructure
-
- sourceId - Variable in class cnslab.cnsnetwork.AFireEvent
-
the avalanche originated from which netHost;
- sourceId - Variable in class cnslab.cnsnetwork.AInputEvent
-
the avalance originated from which netHost.
- sourceId - Variable in class cnslab.cnsnetwork.ANetMessage
-
- sourceId - Variable in class cnslab.cnsnetwork.PInputEvent
-
the source of input id
- sourceTid - Variable in class jpvm.jpvmMessage
-
- SPIKE_ADD - Variable in class cnslab.cnsnetwork.MiNiNeuronPara
-
Additive resets for spike-induced currents
- SPIKE_CURRENT_TO_NB - Variable in class cnslab.cnsnetwork.MiNiNeuronPara
-
Conversion factor between a spike current and the NB term.
- SPIKE_CURRENT_TO_NG - Variable in class cnslab.cnsnetwork.MiNiNeuronPara
-
Conversion factor between a spike current and the NG term.
- SPIKE_CURRENT_TO_SPIKE_NJ - Variable in class cnslab.cnsnetwork.MiNiNeuronPara
-
Conversion factor between a spike current and a spike NJ term.
- SPIKE_RATIO - Variable in class cnslab.cnsnetwork.MiNiNeuronPara
-
Multiplicative resets for spike-induced currents
- SpikeBuffer - Class in cnslab.cnsnetwork
-
Buffer of spikes between min synaptic delay, send all the buffer once.
- SpikeBuffer() - Constructor for class cnslab.cnsnetwork.SpikeBuffer
-
- spikeBuffers - Variable in class cnslab.cnsnetwork.Network
-
spike buffer to store the neuron spikes which needs to be sented
- spikeReceived - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- spikeState - Variable in class cnslab.cnsnetwork.Network
-
flag for trial end
- sta_p - Variable in class cnslab.cnsnetwork.MiNiNeuron
-
two-dimensional array pointing to the state variables.
- sta_p - Variable in class cnslab.cnsnetwork.VSICLIFNeuron
-
pointer to the state variables
- sta_p - Variable in class cnslab.cnsnetwork.VSICLIFNeuronV2
-
pointer to the state variables; the first two states correspond to
the g and b terms respectively, followed by the spike-induced current
terms
- start_button - Variable in class cnslab.gui.mainErnst
-
- starter - Class in <Unnamed>
-
- starter() - Constructor for class starter
-
- startServer() - Method in class cnslab.gui.mainErnst
-
start the JPVM daemon
- startSig - Variable in class cnslab.cnsnetwork.Network
-
trial start flag
- startSimulation(Object) - Method in class cnslab.gui.mainErnst
-
The part starts the main simulation
- state - Variable in class cnslab.cnsnetwork.MiNiNeuron
-
linked list for state variables
- state - Variable in class cnslab.cnsnetwork.VSICLIFNeuron
-
linked list for state variables
- state - Variable in class cnslab.cnsnetwork.VSICLIFNeuronV2
-
linked list for state variables
- status - Variable in class cnslab.gui.mainErnst
-
- stimuli - Variable in class cnslab.cnsnetwork.SubExp
-
stimulus for this subexp
- Stimulus - Class in cnslab.cnsnetwork
-
Stimulus class contains all types of stimulus.
- Stimulus(ModelFactory, SimulatorParser, double, int, double, double, double, double, Seed, int) - Constructor for class cnslab.cnsnetwork.Stimulus
-
- stop() - Method in class cnslab.cnsnetwork.FitFun.ToDo
-
Deprecated.
- stop() - Method in class cnslab.cnsnetwork.MainSimulator.ToDo
-
- stop - Variable in class cnslab.cnsnetwork.Network
-
flag for the computation and communication threads to stop
- stop() - Static method in class cnslab.cnsnetwork.PlotResult
-
- stopRun() - Method in class cnslab.cnsnetwork.Network
-
stop the testRun();
- stopSig - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- stopThread() - Method in class cnslab.cnsnetwork.PMainBK
-
Deprecated.
stop the thread
- StringWrap - Class in cnslab.cnsnetwork
-
Deprecated.
- StringWrap() - Constructor for class cnslab.cnsnetwork.StringWrap
-
Deprecated.
- strm - Variable in class jpvm.jpvmRecvConnection
-
- strm - Variable in class jpvm.jpvmSendConnection
-
- subExp - Variable in class cnslab.cnsnetwork.Experiment
-
array of sub experiments
- SubExp - Class in cnslab.cnsnetwork
-
Subexperiment.
- SubExp(int, double, Stimulus[], Collection<DiscreteEvent>) - Constructor for class cnslab.cnsnetwork.SubExp
-
- subExpId - Variable in class cnslab.cnsnetwork.Network
-
Keep track of current simulated subExp id
- subexpNames - Static variable in class cnslab.cnsnetwork.PlotResult
-
the names of subexperiments
- subexpNames - Variable in class cnslab.cnsnetwork.SimulatorParser
-
Names of sub experiment
- successor() - Method in class cnslab.cnsmath.RBCell
-
Return the inorder successor, or null if no such
- suNames - Variable in class cnslab.cnsnetwork.PlotResult
-
single unit names;
- suNames - Variable in class cnslab.cnsnetwork.Recorder
-
Single unit name array
- suPlot() - Static method in class cnslab.cnsnetwork.PlotResult
-
- suRender - Variable in class cnslab.cnsnetwork.PlotResult
-
- suSeries - Variable in class cnslab.cnsnetwork.PlotResult
-
number of single unit ele
- SWAP(double[], int, int) - Static method in class cnslab.cnsmath.FFT
-
- synapse - Variable in class cnslab.cnsnetwork.PInputEvent
-
the synapse data
- Synapse - Interface in edu.jhu.mb.ernst.model
-
Accessor interface for the neuron synaptic structure.
- SYNAPSE_CURRENT_TO_NB - Variable in class cnslab.cnsnetwork.MiNiNeuronPara
-
Conversion factor between a synapse current and the NB term.
- SYNAPSE_CURRENT_TO_NG - Variable in class cnslab.cnsnetwork.MiNiNeuronPara
-
Conversion factor between a synapse current and the NG term.
- SYNAPSE_CURRENT_TO_SYNAPSE_NJ - Variable in class cnslab.cnsnetwork.MiNiNeuronPara
-
Conversion factor between a synapse current and a synapse NJ term.
- SynapseLib - Class in edu.jhu.mb.ernst.model.synapse
-
Static method library to manipulate Synapse instances.
- synapses - Variable in class cnslab.cnsnetwork.Branch
-
grouped synapses
- syncRoot - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- syncTrialHost - Static variable in interface cnslab.cnsnetwork.NetMessageTag
-
- SYNNeuron - Class in cnslab.cnsnetwork
-
Sync neuron (fake neuron, id is the last neuron index),
used to synchronize between NetHosts, used to send half minimum
synaptic delay time ticks, send buffered spikes
- SYNNeuron(Network) - Constructor for class cnslab.cnsnetwork.SYNNeuron
-