DynamicLib Namespace Reference

DynamicLib. More...

Classes

class AbstractAlgorithm

class AbstractReportHandler

class AbstractSpecificAlgorithmParameter

class Afferent

Afferent. More...

class AfferentNode

class AlgorithmGrid

AlgorithmGrid. More...

class AsciiReportHandler

AsciiReportHandler. More...

class ConfigureNodes

ConfigureNodes. More...

class DynamicLibException

DynamicLibException. All exceptions in DynamicLib derive from here. More...

class DynamicLibTest

Central test class for DynamicLib. More...

class DynamicNetwork

With a DynamicNetwork one can simulate network processes in sparse random networks. More...

class DynamicNetworkImplementation

DynamicNetworkImplementation: an implementation for a Dynamicnetwork, which derives from SparseImplementation. More...

class DynamicNode

class EvolveNodes

EvolveNodes. More...

class InactiveReportHandler

This ReportHandler does nothing, which is sometimes useful in debugging. More...

class IterationNumberException

struct NetworkState

NetworkState. More...

struct NodeInfo

class NodeState

NodeState, the state is calculated by the EvolutionAlgorithm. More...

class RateAlgorithm

RateAlgorithm. More...

class RateFunctor

class ReallocException

struct Report

class RootReportHandler

class SimulationRunParameter

Parameter determining how a simulation is run. Specifiying begin and end time, log file names, etc. More...

class SpatialDynamicNetwork

struct SpatialPosition

class StateConfigurationException

StateConfigurationException. More...

struct WeightedLink

class WilsonCowanAlgorithm

WilsonCowanAlgorithm. More...

struct WilsonCowanParameter

WilsonCowanParameter. More...

Typedefs

typedef AbstractAlgorithm< double > D_AbstractAlgorithm

typedef Afferent< double > D_Afferent

typedef Rate(* RateFunction )(Time)

typedef double Rate

typedef double Time

typedef Time TimeStep

typedef double Density

typedef double Potential

typedef double Efficacy

typedef DynamicNetwork
< DynamicNetworkImplementation
< double > > D_DynamicNetwork

typedef DynamicNode< double > D_DynamicNode

typedef RateAlgorithm< double > D_RateAlgorithm

typedef RateFunctor< double > D_RateFunctor

typedef SpatialDynamicNetwork
< DynamicNetworkImplementation
< double > > D_SpatialNetwork

typedef std::pair< NodeId,
SpatialPosition > NodePosition

typedef WeightedLink< double > D_WeightedLink

Enumerations

enum NodeType { NEUTRAL, EXCITATORY, INHIBITORY }

This gives a DynamicNode's type, which will be checked when Dale's law is set.

enum EvolveResult {
NOT_RUN, SUCCESS, CONFIGURATION_ERROR, EVOLUTION_ERROR,
NUMBER_ITERATIONS_ERROR, REPORT_ERROR
}

enum ReportType { RATE, STATE, UPDATE }

A ReportType specifies whether just a DynamicNode's activation is reported or its full NodeState.

Functions

template<class WeightValue>

ostream & operator<< (ostream &, const AbstractAlgorithm< WeightValue > &)

template<class WeightValue>

istream & operator>> (istream &, AbstractAlgorithm< WeightValue > &)

template<class WeightValue>

ostream & operator<< (ostream &s, DynamicNetwork< WeightValue > &net)

double ToEfficacy (double efficacy)

Standard conversion for operations that depend on efficacy online.

const string STR_ASCIIHANDLER_EXCEPTION ("Could not open ascii handler file stream:")

const string STR_HANDLER_STALE ("This handler already has written reports")

const string STR_DYNAMICLIB_EXCEPTION ("Some DynamicLib exception occurred")

const string STR_STATE_CONFIGURATION_EXCEPTION ("There is a mismatch between the dimension of the State and the EvolutionAlgorithm")

const string STR_ROOTFILE_EXCEPTION ("Couldn't open root file")

const string STR_AE_TAG ("<AbstractAlgorithm>")

const string STR_AE_EXCEPTION ("Can't serialize an AbstractAlgorithm")

const string STR_NETWORKSTATE_TAG ("<NetworkState>")

const string STR_RA_TAG ("<RateAlgorithm>")

const string STR_NETWORKSTATE_ENDTAG ("</NetworkState>")

const string STRING_WC_TAG ("<WilsonCowanAlgorithm>")

const string STR_DYNAMICNETWORKIMPLEMENTATION_TAG ("<DynamicNetworkImplementation>")

const string STR_OPENNETWORKFILE_FAILED ("Could not open test file. Does test directory exist ?")

const string STR_DYNAMIC_NETWORK_TAG ("<DynamicNetwork>")

const string STR_NETWORK_CREATION_FAILED ("Creation of test dynamic network failed")

const string STR_EXCEPTION_CAUSE_UNKNOWN ("Unknow exception thrown in Evolve")

const string STR_NUMBER_ITERATIONS_EXCEEDED ("The predetermined number of iterations is exceeded in Evolve()")

const string STR_INCOMPATIBLE_TIMING_ERROR ("Node Evolve algorithm didn't reach specified end time")

const string STR_TIME ("<Time>")

const string STR_NODEID ("<NodeId>")

const string STR_REPORT ("<Report>")

const string STR_GRID_TAG ("<AlgorithmGrid>")

const string STR_GRID_PARSE_ERROR ("Error parsing AlgorithmGrid")

const string STR_STATE_PARSE_ERROR ("Error parsing NodeState")

const string STR_NODESTATE_TAG ("<NodeState>")

const string STR_DYN_TAG ("<DynamicNode>")

const string STR_WCP_TAG ("<WilsonCowanParameter>")

const string STRING_NODEVALUE ("<NodeValue>")

const string CANVAS_NAME ("Canvas")

const string CANVAS_TITLE ("Dynamic population overview")

const string STR_NETWORK_IMPLEMENTATION_REALLOC ("Network implementation will realloc. This invalidates the internal representation")

const string STR_ROOT_FILE_OPENED_FAILED ("Could not open ROOT file")

const string OFFSET_ERROR ("Cast to DynamicNode failed")

Rate Nul (Time)

ostream & operator<< (ostream &s, const SpatialPosition &pos)

bool operator== (const NodePosition &pos, NodeId id)

allow finding etc by NodeId

bool operator== (const SpatialPosition &p1, const SpatialPosition &p2)

conventional comparison

bool operator!= (const SpatialPosition &p1, const SpatialPosition &p2)

inequality

const string STRING_TEST_DIR ("test/")

const string STRING_WILSONCONWAN_FILE ("WilsonCowan.net")

const string STRING_WILSONCONWAN_ROOTFILE ("WilsonCowan.root")

const string STRING_NODESTATE_STREAMING_TEST ("NodeState.state")

const string STRING_GRID_STREAMING_TEST ("AlgorithmGrid.grid")

const vector< double > WILSON_COWAN_GRID_VECTOR (1, 0)

const AlgorithmGrid WILSON_COWAN_GRID (WILSON_COWAN_GRID_VECTOR, WILSON_COWAN_GRID_VECTOR)

const string STRING_ASCIIREPORTNAME ("WilsonCowan3NodesReport")

const string STRING_OPEN_REPORT_FAILED ("Couldn't open report file")

D_DynamicNetwork WilsonCowanExample ()

Variables

const int HAVE_ROOT = 1

const Time TIME_ROOT_INITIAL_DISPLAY = 0.05

const SpatialPosition INVALID_POSITION

const int RATE_STATE_DIMENSION = 1

Rate Algorithm nodes have a single state.

const int WILSON_COWAN_STATE_DIMENSION = 1

Wilson Cowan nodes have single double as state.

const int WILSON_COWAN_PARAMETER_DIMENSION = 4

The parameter vector for Wilson Cowan integration has four elements.

const double WC_ABSOLUTE_PRECISION = 1e-5

const double WC_RELATIVE_PRECISION = 0

const int N_FRACT_PERCENTAGE_SMALL = 100

const int N_PERCENTAGE_SMALL = 5

const int N_FRACT_PERCENTAGE_BIG = 10

const int CANVAS_X_DIMENSION = 800

const int CANVAS_Y_DIMENSION = 800

const int NUMBER_HISTO_CHANNELS = 500

const Time T_MIN = 0

const Time T_MAX = .04

const Density DENSITY_MIN = -0.1

Density DENSITY_MAX = 50

const Rate F_MIN = -1

const Rate F_MAX = 20

const Potential POTENTIAL_MIN = -0.01

const Potential POTENTIAL_MAX = 0.020

const float FAR_AWAY = std::numeric_limits<float>::max()

const Number NUMBER_OF_RESERVED_NODES = 1000

const double F_NOISE = 1.0

const double AFFERENT = 1.0

const Rate F_RESULT = F_MAX/( 1 + exp(-1*AFFERENT))

const double EPSILON = 1e-6

const Time TIME_MEMBRANE = 5e-3

const double ALPHA = 1

const double BETA = -1.1

const double GAMMA = 2

const double DELTA = -2

const double ETA = -1.5

const Time TAU_EXCITATORY = 10e-3

const Time TAU_INHIBITORY = 5e-3

const Time T_START = 0

const Time T_END = 50e-3

const Time T_STEP = 1e-3

Detailed Description

DynamicLib.


Classes
class	AbstractAlgorithm
class	AbstractReportHandler
class	AbstractSpecificAlgorithmParameter
class	Afferent
	Afferent. More...
class	AfferentNode
class	AlgorithmGrid
	AlgorithmGrid. More...
class	AsciiReportHandler
	AsciiReportHandler. More...
class	ConfigureNodes
	ConfigureNodes. More...
class	DynamicLibException
	DynamicLibException. All exceptions in DynamicLib derive from here. More...
class	DynamicLibTest
	Central test class for DynamicLib. More...
class	DynamicNetwork
	With a DynamicNetwork one can simulate network processes in sparse random networks. More...
class	DynamicNetworkImplementation
	DynamicNetworkImplementation: an implementation for a Dynamicnetwork, which derives from SparseImplementation. More...
class	DynamicNode
class	EvolveNodes
	EvolveNodes. More...
class	InactiveReportHandler
	This ReportHandler does nothing, which is sometimes useful in debugging. More...
class	IterationNumberException
struct	NetworkState
	NetworkState. More...
struct	NodeInfo
class	NodeState
	NodeState, the state is calculated by the EvolutionAlgorithm. More...
class	RateAlgorithm
	RateAlgorithm. More...
class	RateFunctor
class	ReallocException
struct	Report
class	RootReportHandler
class	SimulationRunParameter
	Parameter determining how a simulation is run. Specifiying begin and end time, log file names, etc. More...
class	SpatialDynamicNetwork
struct	SpatialPosition
class	StateConfigurationException
	StateConfigurationException. More...
struct	WeightedLink
class	WilsonCowanAlgorithm
	WilsonCowanAlgorithm. More...
struct	WilsonCowanParameter
	WilsonCowanParameter. More...
Typedefs
typedef AbstractAlgorithm< double >	D_AbstractAlgorithm
typedef Afferent< double >	D_Afferent
typedef Rate(*	RateFunction )(Time)
typedef double	Rate
typedef double	Time
typedef Time	TimeStep
typedef double	Density
typedef double	Potential
typedef double	Efficacy
typedef DynamicNetwork < DynamicNetworkImplementation < double > >	D_DynamicNetwork
typedef DynamicNode< double >	D_DynamicNode
typedef RateAlgorithm< double >	D_RateAlgorithm
typedef RateFunctor< double >	D_RateFunctor
typedef SpatialDynamicNetwork < DynamicNetworkImplementation < double > >	D_SpatialNetwork
typedef std::pair< NodeId, SpatialPosition >	NodePosition
typedef WeightedLink< double >	D_WeightedLink
Enumerations
enum	NodeType { NEUTRAL, EXCITATORY, INHIBITORY }
	This gives a DynamicNode's type, which will be checked when Dale's law is set.
enum	EvolveResult { NOT_RUN, SUCCESS, CONFIGURATION_ERROR, EVOLUTION_ERROR, NUMBER_ITERATIONS_ERROR, REPORT_ERROR }
enum	ReportType { RATE, STATE, UPDATE }
	A ReportType specifies whether just a DynamicNode's activation is reported or its full NodeState.
Functions
template<class WeightValue>
ostream &	operator<< (ostream &, const AbstractAlgorithm< WeightValue > &)
template<class WeightValue>
istream &	operator>> (istream &, AbstractAlgorithm< WeightValue > &)
template<class WeightValue>
ostream &	operator<< (ostream &s, DynamicNetwork< WeightValue > &net)
double	ToEfficacy (double efficacy)
	Standard conversion for operations that depend on efficacy online.
const string	STR_ASCIIHANDLER_EXCEPTION ("Could not open ascii handler file stream:")
const string	STR_HANDLER_STALE ("This handler already has written reports")
const string	STR_DYNAMICLIB_EXCEPTION ("Some DynamicLib exception occurred")
const string	STR_STATE_CONFIGURATION_EXCEPTION ("There is a mismatch between the dimension of the State and the EvolutionAlgorithm")
const string	STR_ROOTFILE_EXCEPTION ("Couldn't open root file")
const string	STR_AE_TAG ("<AbstractAlgorithm>")
const string	STR_AE_EXCEPTION ("Can't serialize an AbstractAlgorithm")
const string	STR_NETWORKSTATE_TAG ("<NetworkState>")
const string	STR_RA_TAG ("<RateAlgorithm>")
const string	STR_NETWORKSTATE_ENDTAG ("</NetworkState>")
const string	STRING_WC_TAG ("<WilsonCowanAlgorithm>")
const string	STR_DYNAMICNETWORKIMPLEMENTATION_TAG ("<DynamicNetworkImplementation>")
const string	STR_OPENNETWORKFILE_FAILED ("Could not open test file. Does test directory exist ?")
const string	STR_DYNAMIC_NETWORK_TAG ("<DynamicNetwork>")
const string	STR_NETWORK_CREATION_FAILED ("Creation of test dynamic network failed")
const string	STR_EXCEPTION_CAUSE_UNKNOWN ("Unknow exception thrown in Evolve")
const string	STR_NUMBER_ITERATIONS_EXCEEDED ("The predetermined number of iterations is exceeded in Evolve()")
const string	STR_INCOMPATIBLE_TIMING_ERROR ("Node Evolve algorithm didn't reach specified end time")
const string	STR_TIME ("<Time>")
const string	STR_NODEID ("<NodeId>")
const string	STR_REPORT ("<Report>")
const string	STR_GRID_TAG ("<AlgorithmGrid>")
const string	STR_GRID_PARSE_ERROR ("Error parsing AlgorithmGrid")
const string	STR_STATE_PARSE_ERROR ("Error parsing NodeState")
const string	STR_NODESTATE_TAG ("<NodeState>")
const string	STR_DYN_TAG ("<DynamicNode>")
const string	STR_WCP_TAG ("<WilsonCowanParameter>")
const string	STRING_NODEVALUE ("<NodeValue>")
const string	CANVAS_NAME ("Canvas")
const string	CANVAS_TITLE ("Dynamic population overview")
const string	STR_NETWORK_IMPLEMENTATION_REALLOC ("Network implementation will realloc. This invalidates the internal representation")
const string	STR_ROOT_FILE_OPENED_FAILED ("Could not open ROOT file")
const string	OFFSET_ERROR ("Cast to DynamicNode failed")
Rate	Nul (Time)
ostream &	operator<< (ostream &s, const SpatialPosition &pos)
bool	operator== (const NodePosition &pos, NodeId id)
	allow finding etc by NodeId
bool	operator== (const SpatialPosition &p1, const SpatialPosition &p2)
	conventional comparison
bool	operator!= (const SpatialPosition &p1, const SpatialPosition &p2)
	inequality
const string	STRING_TEST_DIR ("test/")
const string	STRING_WILSONCONWAN_FILE ("WilsonCowan.net")
const string	STRING_WILSONCONWAN_ROOTFILE ("WilsonCowan.root")
const string	STRING_NODESTATE_STREAMING_TEST ("NodeState.state")
const string	STRING_GRID_STREAMING_TEST ("AlgorithmGrid.grid")
const vector< double >	WILSON_COWAN_GRID_VECTOR (1, 0)
const AlgorithmGrid	WILSON_COWAN_GRID (WILSON_COWAN_GRID_VECTOR, WILSON_COWAN_GRID_VECTOR)
const string	STRING_ASCIIREPORTNAME ("WilsonCowan3NodesReport")
const string	STRING_OPEN_REPORT_FAILED ("Couldn't open report file")
D_DynamicNetwork	WilsonCowanExample ()
Variables
const int	HAVE_ROOT = 1
const Time	TIME_ROOT_INITIAL_DISPLAY = 0.05
const SpatialPosition	INVALID_POSITION
const int	RATE_STATE_DIMENSION = 1
	Rate Algorithm nodes have a single state.
const int	WILSON_COWAN_STATE_DIMENSION = 1
	Wilson Cowan nodes have single double as state.
const int	WILSON_COWAN_PARAMETER_DIMENSION = 4
	The parameter vector for Wilson Cowan integration has four elements.
const double	WC_ABSOLUTE_PRECISION = 1e-5
const double	WC_RELATIVE_PRECISION = 0
const int	N_FRACT_PERCENTAGE_SMALL = 100
const int	N_PERCENTAGE_SMALL = 5
const int	N_FRACT_PERCENTAGE_BIG = 10
const int	CANVAS_X_DIMENSION = 800
const int	CANVAS_Y_DIMENSION = 800
const int	NUMBER_HISTO_CHANNELS = 500
const Time	T_MIN = 0
const Time	T_MAX = .04
const Density	DENSITY_MIN = -0.1
Density	DENSITY_MAX = 50
const Rate	F_MIN = -1
const Rate	F_MAX = 20
const Potential	POTENTIAL_MIN = -0.01
const Potential	POTENTIAL_MAX = 0.020
const float	FAR_AWAY = std::numeric_limits<float>::max()
const Number	NUMBER_OF_RESERVED_NODES = 1000
const double	F_NOISE = 1.0
const double	AFFERENT = 1.0
const Rate	F_RESULT = F_MAX/( 1 + exp(-1*AFFERENT))
const double	EPSILON = 1e-6
const Time	TIME_MEMBRANE = 5e-3
const double	ALPHA = 1
const double	BETA = -1.1
const double	GAMMA = 2
const double	DELTA = -2
const double	ETA = -1.5
const Time	TAU_EXCITATORY = 10e-3
const Time	TAU_INHIBITORY = 5e-3
const Time	T_START = 0
const Time	T_END = 50e-3
const Time	T_STEP = 1e-3