Basic Electrophysiology Relacs Plugins  0.9.8
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
NeuronModels Class Reference

#include <neuronmodels.h>

Inheritance diagram for NeuronModels:
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Collaboration diagram for NeuronModels:
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Public Member Functions

 NeuronModels (void)
 
 NeuronModels (const string &name, const string &pluginset="", const string &author="unknown", const string &version="unknown", const string &date=__DATE__)
 
virtual ~NeuronModels (void)
 
virtual void main (void)
 
virtual void process (const OutData &source, OutData &dest)
 
virtual void operator() (double t, double *x, double *dxdt, int n)
 
virtual Options metaData (void)
 
double timeStep (void) const
 
void setTimeStep (double deltat)
 
double noiseD (void) const
 
void setNoiseD (double noised)
 
double noiseFac (void) const
 
void setNoiseFac (void)
 
SpikingNeuron * neuron (void) const
 
void add (SpikingNeuron *model, const string &title="")
 
void addModels (void)
 
void addOptions (void)
 
void readOptions (void)
 
- Public Member Functions inherited from Model
 Model (const string &name, const string &pluginset="", const string &author="unknown", const string &version="unknown", const string &date=__DATE__)
 
virtual ~Model (void)
 
virtual void notify (void)
 
double signal (double t, int trace=0) const
 
bool interrupt (void) const
 
bool isRunning (void) const
 
void push (int trace, float val)
 
void next (void)
 
int traces (void) const
 
string traceName (int trace) const
 
double deltat (int trace) const
 
double time (int trace) const
 
float scale (int trace) const
 
void waitOnSignals (void)
 
double load (void) const
 
virtual void addActions (QMenu *menu, bool doxydoc)
 
virtual void setName (const string &name)
 
- Public Member Functions inherited from ConfigDialog
 ConfigDialog (const string &configident="", int configgroup=0, const string &name="", const string &author="", const string &version="", const string &date=__DATE__)
 
virtual ~ConfigDialog (void)
 
string name (void) const
 
string author (void) const
 
virtual void setAuthor (const string &author)
 
string version (void) const
 
virtual void setVersion (const string &version)
 
string date (void) const
 
virtual void setDate (const string &date)
 
virtual void dialogButtons (OptDialog *od)
 
virtual void dialogEmptyMessage (OptDialog *od)
 
int dialogSelectMask (void) const
 
void setDialogSelectMask (int mask)
 
void addDialogSelectMask (int mask)
 
int dialogReadOnlyMask (void) const
 
void setDialogReadOnlyMask (int mask)
 
void addDialogReadOnlyMask (int mask)
 
int dialogStyle (void) const
 
void setDialogStyle (int style)
 
void addDialogStyle (int style)
 
string dialogCaption (void) const
 
void setDialogCaption (const string &caption)
 
bool dialogHeader (void) const
 
void setDialogHeader (bool d)
 
string headerBackgroundColor (void) const
 
void setHeaderBackgroundColor (const string &color)
 
string headerForegroundColor (void) const
 
void setHeaderForegroundColor (const string &color)
 
string headerImageFile (void) const
 
void setHeaderImageFile (const string &file)
 
virtual void dialogHeaderWidget (OptDialog *od)
 
bool dialogHelp (void) const
 
void setDialogHelp (bool d)
 
string helpCaption (void) const
 
void setHelpCaption (const string &caption)
 
string helpPath (int inx=0) const
 
int helpPathes (void) const
 
void clearHelpPathes (void)
 
void setHelpPath (const string &path)
 
void addHelpPath (const string &path)
 
virtual string helpFileName (void) const
 
bool dialogOpen (void) const
 
bool helpOpen (void) const
 
QWidget * mainWidget (void)
 
virtual void setMainWidget (QWidget *widget)
 
void lock () const
 
void unlock () const
 
bool tryLock (int timeout=1)
 
QMutex * mutex (void)
 
- Public Member Functions inherited from ConfigClass
 ConfigClass (const string &ident, int group=0, int mode=0xffff, int selectmask=0)
 
 ConfigClass (const ConfigClass &C)
 
virtual ~ConfigClass (void)
 
const string & configIdent (void) const
 
void setConfigIdent (const string &ident)
 
int configGroup (void) const
 
void setConfigGroup (int group)
 
int configMode (void) const
 
void setConfigMode (int mode)
 
void addConfigMode (int mode)
 
void delConfigMode (int mode)
 
int configSelectMask (void) const
 
void setConfigSelectMask (int mask)
 
void addConfig (void)
 
void readConfig (void)
 
virtual void readConfig (StrQueue &sq)
 
virtual void saveConfig (ofstream &str)
 
virtual int configSize (void) const
 
virtual void config (void)
 
virtual void preConfig (void)
 

Protected Member Functions

void dialogModelOptions (OptDialog *od, string *tabhotkeys)
 
virtual OptWidget * dialogOptions (OptDialog *od, string *tabhotkeys=0)
 
- Protected Member Functions inherited from ConfigDialog
void setDialogOpen (bool open=true)
 
void setHelpOpen (bool open=true)
 

Protected Attributes

void(* Integrate )(double, double *, double *, int, double, NeuronModels &)
 
double CurrentInput
 
double GMC
 
double EMC
 
double MVMC
 
double MWMC
 
double TAUMC
 
int MMCInx
 
double GMHC
 
double EMHC
 
double MVMHC
 
double MWMHC
 
double TAUMMHC
 
double PMMHC
 
int MMHCInx
 
double HVMHC
 
double HWMHC
 
double TAUHMHC
 
double PHMHC
 
int HMHCInx
 
- Protected Attributes inherited from ConfigDialog
Options DialogOptions
 

Additional Inherited Members

- Public Types inherited from ConfigClass
enum  Action
 
- Public Slots inherited from ConfigDialog
virtual void dialog (void)
 
virtual void help (void)
 
virtual void notifyDialog (const Options &opt)
 
- Signals inherited from ConfigDialog
void dialogAccepted (void)
 
void dialogAction (int r)
 
void dialogClosed (int r)
 
- Static Public Member Functions inherited from ConfigClass
static void setConfigureClasses (ConfigureClasses *cfg)
 
- Protected Slots inherited from ConfigDialog
void notificationFromDialog (const Parameter &p)
 
virtual void dClosed (int r)
 
virtual void hClosed (int r)
 

Detailed Description

[Model] Various models of conductance-based spiking (point-) neurons.

Author
Jan Benda
Alexander Wolf
Version
1.2 (Jul 11, 2012)

The Gaussian white noise and the optional additional voltage gated currents are added to the input after the offset and gain for the input current has been applied.

Options
  • Spike generator
  • spikemodel=Stimulus: Spike model (string)
  • noised=0: Intensity of current noise (number)
  • deltat=0.005ms: Delta t (number)
  • integrator=Euler: Method of integration (string)
  • Voltage-gated current 1 (activation only)
  • gmc=0: Conductivity (number)
  • emc=-90mV: Reversal potential (number)
  • mvmc=-40mV: Midpoint potential of activation (number)
  • mwmc=10mV: Width of activation (number)
  • taumc=10ms: Time constant (number)
  • Voltage-gated current 2 (activation and inactivation)
  • gmhc=0: Conductivity (number)
  • emhc=-90mV: Reversal potential (number)
  • mvmhc=-40mV: Midpoint potential of activation (number)
  • mwmhc=10mV: Width of activation (number)
  • taummhc=10ms: Time constant of activation (number)
  • pmmhc=1: Power of activation gate (number)
  • hvmhc=-40mV: Midpoint potential of inactivation (number)
  • hwmhc=10mV: Width of inactivation (number)
  • tauhmhc=10ms: Time constant of inactivation (number)
  • pmhhc=1: Power of inactivation gate (number)

Constructor & Destructor Documentation

NeuronModels ( void  )

References NeuronModels::addModels(), NeuronModels::addOptions(), NeuronModels::HMHCInx, NeuronModels::MMCInx, and NeuronModels::MMHCInx.

NeuronModels ( const string &  name,
const string &  pluginset = "",
const string &  author = "unknown",
const string &  version = "unknown",
const string &  date = __DATE__ 
)
~NeuronModels ( void  )
virtual

Member Function Documentation

void main ( void  )
virtual

Reimplemented from Model.

References NeuronModels::CurrentInput, Model::deltat(), SpikingNeuron::dimension(), floor(), NeuronModels::GMC, NeuronModels::GMHC, NeuronModels::HMHCInx, SpikingNeuron::init(), NeuronModels::Integrate, Model::interrupt(), NeuronModels::MMCInx, NeuronModels::MMHCInx, NeuronModels::neuron(), Model::next(), Model::push(), NeuronModels::readOptions(), NeuronModels::setNoiseFac(), NeuronModels::setTimeStep(), Model::time(), NeuronModels::timeStep(), Model::traceName(), and Model::traces().

void process ( const OutData &  source,
OutData &  dest 
)
virtual

Reimplemented from Model.

void operator() ( double  t,
double *  x,
double *  dxdt,
int  n 
)
virtual

References NeuronModels::CurrentInput, NeuronModels::EMC, NeuronModels::EMHC, exp(), SpikingNeuron::gain(), NeuronModels::GMC, NeuronModels::GMHC, NeuronModels::HMHCInx, NeuronModels::HVMHC, NeuronModels::HWMHC, NeuronModels::MMCInx, NeuronModels::MMHCInx, NeuronModels::MVMC, NeuronModels::MVMHC, NeuronModels::MWMC, NeuronModels::MWMHC, NeuronModels::noiseFac(), SpikingNeuron::offset(), NeuronModels::PHMHC, NeuronModels::PMMHC, Model::signal(), NeuronModels::TAUHMHC, NeuronModels::TAUMC, and NeuronModels::TAUMMHC.

Options metaData ( void  )
virtual

Reimplemented from Model.

References ConfigClass::configIdent(), and SpikingNeuron::name().

double timeStep ( void  ) const
inline

The integration time step.

Referenced by NeuronModels::main().

void setTimeStep ( double  deltat)
inline

Set the integration time step to deltat.

Referenced by NeuronModels::main(), and NeuronModels::readOptions().

double noiseD ( void  ) const
inline

The intensity of the noise.

void setNoiseD ( double  noised)
inline

Set the intensity of the noise to noised.

Referenced by NeuronModels::readOptions().

double noiseFac ( void  ) const
inline

The prefactor for the Gaussian noise to get the noise intensity noiseD().

Referenced by NeuronModels::operator()().

void setNoiseFac ( void  )
inline

References relacs::sqrt().

Referenced by NeuronModels::main().

SpikingNeuron* neuron ( void  ) const
inline

The active Spiking Neuron model.

Referenced by NeuronModels::main().

void add ( SpikingNeuron *  model,
const string &  title = "" 
)

Add a SpikingNeuron model

References SpikingNeuron::add(), SpikingNeuron::name(), ConfigClass::setConfigGroup(), and ConfigClass::setConfigIdent().

Referenced by NeuronModels::addModels().

void addModels ( void  )

Add all SpikingNeuron models.

References NeuronModels::add().

Referenced by NeuronModels::NeuronModels().

void addOptions ( void  )

Add some general options for integrating SpikingNeuron models such as time step, integration method, and the neuron model.

Referenced by NeuronModels::NeuronModels().

void readOptions ( void  )

Read the general options for integrating SpikingNeuron models such as time step, integration method, neuron model and its options.

References NeuronModels::EMC, NeuronModels::EMHC, eulerStep(), NeuronModels::GMC, NeuronModels::GMHC, NeuronModels::HVMHC, NeuronModels::HWMHC, NeuronModels::Integrate, midpointStep(), NeuronModels::MVMC, NeuronModels::MVMHC, NeuronModels::MWMC, NeuronModels::MWMHC, SpikingNeuron::notify(), NeuronModels::PHMHC, NeuronModels::PMMHC, rk4Step(), NeuronModels::setNoiseD(), NeuronModels::setTimeStep(), NeuronModels::TAUHMHC, NeuronModels::TAUMC, and NeuronModels::TAUMMHC.

Referenced by NeuronModels::main().

void dialogModelOptions ( OptDialog *  od,
string *  tabhotkeys 
)
protected

Add the options of the models as tabs to the dialog od. To be used in dialogOptions().

References OptDialog::addTabOptions(), ConfigDialog::dialogReadOnlyMask(), ConfigDialog::dialogSelectMask(), ConfigDialog::dialogStyle(), and ConfigDialog::mutex().

Referenced by NeuronModels::dialogOptions().

OptWidget * dialogOptions ( OptDialog *  od,
string *  tabhotkeys = 0 
)
protectedvirtual

Reimplemented from ConfigDialog.

References OptDialog::addTabOptions(), NeuronModels::dialogModelOptions(), ConfigDialog::dialogReadOnlyMask(), ConfigDialog::dialogSelectMask(), ConfigDialog::dialogStyle(), ConfigDialog::mutex(), and OptDialog::setVerticalSpacing().

Member Data Documentation

void(* Integrate)(double, double *, double *, int, double, NeuronModels &)
protected

Referenced by NeuronModels::main(), and NeuronModels::readOptions().

double CurrentInput
protected

Referenced by NeuronModels::main(), and NeuronModels::operator()().

double GMC
protected

Referenced by NeuronModels::main(), NeuronModels::operator()(), and NeuronModels::readOptions().

double EMC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double MVMC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double MWMC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double TAUMC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

int MMCInx
protected

Referenced by NeuronModels::main(), NeuronModels::NeuronModels(), and NeuronModels::operator()().

double GMHC
protected

Referenced by NeuronModels::main(), NeuronModels::operator()(), and NeuronModels::readOptions().

double EMHC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double MVMHC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double MWMHC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double TAUMMHC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double PMMHC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

int MMHCInx
protected

Referenced by NeuronModels::main(), NeuronModels::NeuronModels(), and NeuronModels::operator()().

double HVMHC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double HWMHC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double TAUHMHC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

double PHMHC
protected

Referenced by NeuronModels::operator()(), and NeuronModels::readOptions().

int HMHCInx
protected

Referenced by NeuronModels::main(), NeuronModels::NeuronModels(), and NeuronModels::operator()().

The documentation for this class was generated from the following files:
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