SimulatorParser (ERNST API)

java.lang.Object
- cnslab.cnsnetwork.SimulatorParser

```
public final class SimulatorParser
extends Object
```
Simulator Parser, to parse XML file

Version:

$Date: 2012-08-04 15:43:19 -0500 (Sat, 04 Aug 2012) $ $Rev: 117 $ $Author: jmcohen27 $

Author:

Yi Dong, David Wallace Croft, M.Sc., Jeremy Cohen

Field Summary

Fields
Modifier and Type	Field and Description
`int`	`aSec`
`double`	`backgroundFrequency` background firing rate
`double`	`backgroundStrength` background synaptic strength
`int`	`bChannel` background inputs channel
`int`	`bSec`
`Document`	`document`
`DocumentType`	`documentType`
`Map<String,Double>`	`doubleDataMap` Double Data defined in Data section of XML file
`Experiment`	`experiment`
`Seed`	`idum` seed number
`LayerStructure`	`layerStructure` Layer structure
`int`	`mapType` cell map type abmap or linemap
`Map<String,double[][]>`	`matrixDataMap` Matrix Data defined in Data section of XML file
`double`	`minDelay` minimum synaptic delay
`Map<String,Para>`	`modelParaMap` Model parameters
`int`	`numOfHosts` number of Hosts;
`String`	`outFile` output file name
`PrintStream`	`p`
`int`	`parallelHost` number of parallel hosts
`Element`	`rootElement`
`ArrayList<String>`	`subexpNames` Names of sub experiment
`int`	`xEdgeLength` length of xEdge
`int`	`yEdgeLength` length of yEdge

Constructor Summary

Constructors
Constructor and Description
`SimulatorParser()`
`SimulatorParser(Seed idum, Document doc)`
`SimulatorParser(Seed idum, File modelFile)`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`findMinDelay()` Find out the minimum synaptic delay from network structure.
`DiscreteEventQueue`	`getDiscreteEventQueue()`
`EngineFactory`	`getEngineFactory()`
`ModelFactory`	`getModelFactory()`
`Seq<ModulatedSynapse>`	`getModulatedSynapseSeq()`
`static void`	`main(String[] args)`
`double`	`parseChangeConnection(int hostId)` Deprecated.
`double`	`parseConnection()` Parse the connection section, connect the neurons and build up the network structure
`double`	`parseConnection(int hostId)` Parse the connection section, connect the neurons and build up the network structure
`void`	`parseExp(int hostId)` Parse the experiment section, build stimuli accordingly
`void`	`parseExperiment()` Parse the experiment for main host
`void`	`parseMapCells()` Map the cells and build up the index, for main host.
`void`	`parseMapCells(int hostId)` map the neurons, build up the index
`Collection<DiscreteEvent>`	`parseModulator(Element subExperimentElement)`
`void`	`parseNeuronDef()` Parse the neuron definition, for main host.
`void`	`parsePopNeurons()` populate the neurons for main host, minimum memory useage
`void`	`parsePopNeurons(int hostId)` populate the neurons for net host
`void`	`parseScaffold(int hostId)` Build the scaffold.
`void`	`parseTarget(JpvmInfo info)` set the target host id.
`void`	`referenceCheck()` Check XML reference is good or not
`String`	`validate(File modelFile)` Check whether the XML file is valid or not
`String`	`validate(String modelFilename)` Check whether the XML file is valid or not

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

p
```
public PrintStream p
```

minDelay
```
public double minDelay
```
minimum synaptic delay

experiment
```
public Experiment experiment
```

layerStructure
```
public LayerStructure layerStructure
```
Layer structure

idum
```
public Seed idum
```
seed number

xEdgeLength
```
public int xEdgeLength
```
length of xEdge

yEdgeLength
```
public int yEdgeLength
```
length of yEdge

numOfHosts
```
public int numOfHosts
```
number of Hosts;

mapType
```
public int mapType
```
cell map type abmap or linemap

parallelHost
```
public int parallelHost
```
number of parallel hosts

aSec
```
public int aSec
```

bSec
```
public int bSec
```

backgroundFrequency
```
public double backgroundFrequency
```
background firing rate

backgroundStrength
```
public double backgroundStrength
```
background synaptic strength

bChannel
```
public int bChannel
```
background inputs channel

outFile
```
public String outFile
```
output file name

document
```
public Document document
```

rootElement
```
public Element rootElement
```

documentType
```
public DocumentType documentType
```

subexpNames
```
public ArrayList<String> subexpNames
```
Names of sub experiment

modelParaMap
```
public Map<String,Para> modelParaMap
```
Model parameters

doubleDataMap
```
public Map<String,Double> doubleDataMap
```
Double Data defined in Data section of XML file

matrixDataMap
```
public Map<String,double[][]> matrixDataMap
```
Matrix Data defined in Data section of XML file

Constructor Detail

SimulatorParser

public SimulatorParser(Seed idum,
               File modelFile)

SimulatorParser

public SimulatorParser(Seed idum,
               Document doc)

SimulatorParser
```
public SimulatorParser()
```

Method Detail
- main
```
public static void main(String[] args)
                 throws Exception
```
  Throws:
  
  Exception
- getDiscreteEventQueue
```
public DiscreteEventQueue getDiscreteEventQueue()
```
- getEngineFactory
```
public EngineFactory getEngineFactory()
```
- getModelFactory
```
public ModelFactory getModelFactory()
```
- getModulatedSynapseSeq
```
public Seq<ModulatedSynapse> getModulatedSynapseSeq()
```
- validate
```
public String validate(String modelFilename)
```
  Check whether the XML file is valid or not
- validate
```
public String validate(File modelFile)
```
  Check whether the XML file is valid or not
- referenceCheck
```
public void referenceCheck()
```
  Check XML reference is good or not
- parseConnection
```
public double parseConnection()
                       throws Exception
```
  Parse the connection section, connect the neurons and build up the network structure
  
  Throws:
  
  Exception
- parseScaffold
```
public void parseScaffold(int hostId)
                   throws Exception
```
  Build the scaffold. This method is called by NetHost.createSimulatorParser().
  
  Throws:
  
  Exception
- parseChangeConnection
```
@Deprecated
public double parseChangeConnection(int hostId)
                             throws Exception
```
  Deprecated.
  
  Throws:
  
  Exception
- parseConnection
```
public double parseConnection(int hostId)
                       throws Exception
```
  Parse the connection section, connect the neurons and build up the network structure
  
  Throws:
  
  Exception
- parseMapCells
```
public void parseMapCells(int hostId)
```
  map the neurons, build up the index
- parseExp
```
public void parseExp(int hostId)
```
  Parse the experiment section, build stimuli accordingly
- findMinDelay
```
public void findMinDelay()
```
  Find out the minimum synaptic delay from network structure.
- parseExperiment
```
public void parseExperiment()
```
  Parse the experiment for main host
- parseMapCells
```
public void parseMapCells()
```
  Map the cells and build up the index, for main host. Called by class MainSimulator method run().
- parseModulator
```
public Collection<DiscreteEvent> parseModulator(Element subExperimentElement)
```
- parseNeuronDef
```
public void parseNeuronDef()
```
  Parse the neuron definition, for main host.
- parsePopNeurons
```
public void parsePopNeurons(int hostId)
```
  populate the neurons for net host
- parsePopNeurons
```
public void parsePopNeurons()
```
  populate the neurons for main host, minimum memory useage
- parseTarget
```
public void parseTarget(JpvmInfo info)
                 throws jpvmException
```
  set the target host id.
  
  Throws:
  
  jpvmException

Class SimulatorParser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

p

minDelay

experiment

layerStructure

idum

xEdgeLength

yEdgeLength

numOfHosts

mapType

parallelHost

aSec

bSec

backgroundFrequency

backgroundStrength

bChannel

outFile

document

rootElement

documentType

subexpNames

modelParaMap

doubleDataMap

matrixDataMap

Constructor Detail

SimulatorParser

SimulatorParser

SimulatorParser

Method Detail

main

getDiscreteEventQueue

getEngineFactory

getModelFactory

getModulatedSynapseSeq

validate

validate

referenceCheck

parseConnection

parseScaffold

parseChangeConnection

parseConnection

parseMapCells

parseExp

findMinDelay

parseExperiment

parseMapCells

parseModulator

parseNeuronDef

parsePopNeurons

parsePopNeurons

parseTarget