PropagationPropertiesCalculator Class Reference

#include <PropagationPropertiesCalculator.hpp>

Collaboration diagram for PropagationPropertiesCalculator:

List of all members.

Public Member Functions

PropagationPropertiesCalculator (Hdf5DataReader *pDataReader, const std::string voltageName="V")

double CalculateMaximumUpstrokeVelocity (unsigned globalNodeIndex)

std::vector< double > CalculateAllMaximumUpstrokeVelocities (unsigned globalNodeIndex, double threshold)

std::vector< double > CalculateUpstrokeTimes (unsigned globalNodeIndex, double threshold)

double CalculateConductionVelocity (unsigned globalNearNodeIndex, unsigned globalFarNodeIndex, const double euclideanDistance)

std::vector< double > CalculateAllConductionVelocities (unsigned globalNearNodeIndex, unsigned globalFarNodeIndex, const double euclideanDistance)

double CalculateActionPotentialDuration (const double percentage, unsigned globalNodeIndex)

double CalculatePeakMembranePotential (unsigned globalNodeIndex)

std::vector< double > CalculateAllActionPotentialDurations (const double percentage, unsigned globalNodeIndex, double threshold)

std::vector< unsigned > CalculateAllAboveThresholdDepolarisations (unsigned globalNodeIndex, double threshold)

unsigned CalculateAboveThresholdDepolarisationsForLastAp (unsigned globalNodeIndex, double threshold)

Private Member Functions

std::vector< double > & rCacheVoltages (unsigned globalNodeIndex)

Private Attributes

Hdf5DataReader * mpDataReader

const std::string mVoltageName

std::vector< double > mTimes

unsigned mCachedNodeGlobalIndex

std::vector< double > mCachedVoltages

Detailed Description

Calculate physiological properties at given global mesh indices

maximum upstroke velocity at a single cell
times of upstroke at a single cell
(all) conduction velocities between two cells
(all) action potential duration at a single cell
maximum transmembrane potential (maximum systolic potential) at a single cell.

Definition at line 44 of file PropagationPropertiesCalculator.hpp.

Constructor & Destructor Documentation

PropagationPropertiesCalculator::PropagationPropertiesCalculator	(	Hdf5DataReader *	pDataReader,
		const std::string	voltageName = `"V"`
	)

Constructor.

Parameters:

	pDataReader	Pointer to the data reader containing the simulation.
	voltageName	Optionally the name of the variable representing the membrane potential. Defaults to "V".

Definition at line 35 of file PropagationPropertiesCalculator.cpp.

Member Function Documentation

std::vector< double > & PropagationPropertiesCalculator::rCacheVoltages ( unsigned globalNodeIndex ) [private]

Read the voltages vector for the given node and cache it, returning a reference to the cached vector. If subsequently called with the same index, will return the cached vector without re-reading from file.

Note: will only cache the last node index used.

Parameters:

globalNodeIndex

the index of the node to cache voltages for

Definition at line 239 of file PropagationPropertiesCalculator.cpp.

References Hdf5DataReader::GetVariableOverTime(), mCachedNodeGlobalIndex, mCachedVoltages, mpDataReader, and mVoltageName.

Referenced by CalculateAboveThresholdDepolarisationsForLastAp(), CalculateActionPotentialDuration(), CalculateAllAboveThresholdDepolarisations(), CalculateAllActionPotentialDurations(), CalculateAllConductionVelocities(), CalculateAllMaximumUpstrokeVelocities(), CalculateConductionVelocity(), CalculateMaximumUpstrokeVelocity(), CalculatePeakMembranePotential(), and CalculateUpstrokeTimes().

double PropagationPropertiesCalculator::CalculateMaximumUpstrokeVelocity ( unsigned globalNodeIndex )

Calculate the maximum upstroke velocity at a single cell. We calculate for the last upstroke found in the simulation data.

Parameters:

globalNodeIndex

The cell at which to calculate.

Definition at line 48 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetLastMaxUpstrokeVelocity(), mTimes, and rCacheVoltages().

std::vector< double > PropagationPropertiesCalculator::CalculateAllMaximumUpstrokeVelocities	(	unsigned	globalNodeIndex,
		double	threshold
	)

Calculate the maximum upstroke velocity at a single cell. We return all the max upstroke velocities for all APs.

Parameters:

	globalNodeIndex	The cell at which to calculate.
	threshold	The voltage threshold (we use this for marking the end of an AP)

Definition at line 55 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetMaxUpstrokeVelocities(), mTimes, and rCacheVoltages().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteAboveThresholdDepolarisationFile(), and PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteMaxUpstrokeVelocityMap().

std::vector< double > PropagationPropertiesCalculator::CalculateUpstrokeTimes	(	unsigned	globalNodeIndex,
		double	threshold
	)

Calculate the times of upstroke at a single cell. We return all the times of upstroke velocities for all APs.

Parameters:

	globalNodeIndex	The cell at which to calculate.
	threshold	The voltage threshold for APD calculation (we count this as the start of an AP)

Definition at line 62 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetTimesAtMaxUpstrokeVelocity(), mTimes, and rCacheVoltages().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteUpstrokeTimeMap().

double PropagationPropertiesCalculator::CalculateConductionVelocity	(	unsigned	globalNearNodeIndex,
		unsigned	globalFarNodeIndex,
		const double	euclideanDistance
	)

Calculate the conduction velocity between two cells, i.e. the time taken for an AP to propagate from one to the other. It returns the value of conduction velocity of the LAST action potential that reached both nodes. Throws exceptions if an AP never reached one of the nodes.

Parameters:

	globalNearNodeIndex	The cell to measure from.
	globalFarNodeIndex	The cell to measure to.
	euclideanDistance	The distance the AP travels between the cells, along the tissue.

Definition at line 104 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetMaxUpstrokeVelocities(), CellProperties::GetTimeAtLastMaxUpstrokeVelocity(), CellProperties::GetTimesAtMaxUpstrokeVelocity(), Hdf5DataReader::GetVariableOverTime(), mpDataReader, mTimes, mVoltageName, and rCacheVoltages().

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge().

std::vector< double > PropagationPropertiesCalculator::CalculateAllConductionVelocities	(	unsigned	globalNearNodeIndex,
		unsigned	globalFarNodeIndex,
		const double	euclideanDistance
	)

Calculate all the conduction velocities between two cells, i.e. the time taken for all APs to propagate from one to the other. It returns a vector containing all the conduction velocities for each of the APs that reached the two nodes (only the APs that reached both nodes). Throws exceptions if an AP never reached one of the nodes.

Parameters:

	globalNearNodeIndex	The cell to measure from.
	globalFarNodeIndex	The cell to measure to.
	euclideanDistance	The distance the AP travels between the cells, along the tissue.

Definition at line 159 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetTimesAtMaxUpstrokeVelocity(), Hdf5DataReader::GetVariableOverTime(), mpDataReader, mTimes, mVoltageName, and rCacheVoltages().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteConductionVelocityMap().

double PropagationPropertiesCalculator::CalculateActionPotentialDuration	(	const double	percentage,
		unsigned	globalNodeIndex
	)

Calculate the action potential duration at a single cell. We calculate for the last AP found in the simulation data.

Parameters:

	percentage	The percentage of the amplitude to calculate for.
	globalNodeIndex	The cell at which to calculate.

Definition at line 69 of file PropagationPropertiesCalculator.cpp.

References EXCEPTION, CellProperties::GetLastActionPotentialDuration(), mTimes, and rCacheVoltages().

Referenced by AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge().

double PropagationPropertiesCalculator::CalculatePeakMembranePotential ( unsigned globalNodeIndex )

Calculate the maximum transmembrane potential (maximum systolic potential) at a single cell. We calculate for the last AP found in the simulation data.

Parameters:

globalNodeIndex

The cell at which to calculate.

Definition at line 90 of file PropagationPropertiesCalculator.cpp.

References rCacheVoltages().

std::vector< double > PropagationPropertiesCalculator::CalculateAllActionPotentialDurations	(	const double	percentage,
		unsigned	globalNodeIndex,
		double	threshold
	)

Calculate all the action potentials duration at a single cell.

Parameters:

	percentage	The percentage of the amplitude to calculate for.
	globalNodeIndex	The cell at which to calculate.
	threshold	The voltage threshold for APD calculation (we count this as the start of an AP)

Definition at line 81 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetAllActionPotentialDurations(), mTimes, and rCacheVoltages().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteApdMapFile().

std::vector< unsigned > PropagationPropertiesCalculator::CalculateAllAboveThresholdDepolarisations	(	unsigned	globalNodeIndex,
		double	threshold
	)

Calculates all the depolarisations that occur above threshold at a single cell.

Parameters:

	globalNodeIndex	the cell at which to calculate
	threshold	the threshold above which the depolarisations are counted

Definition at line 223 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetNumberOfAboveThresholdDepolarisationsForAllAps(), mTimes, and rCacheVoltages().

Referenced by PostProcessingWriter< ELEMENT_DIM, SPACE_DIM >::WriteAboveThresholdDepolarisationFile().

unsigned PropagationPropertiesCalculator::CalculateAboveThresholdDepolarisationsForLastAp	(	unsigned	globalNodeIndex,
		double	threshold
	)

Calculates the depolarisations that occur above threshold at a single cell during the last recorded Ap

Parameters:

	globalNodeIndex	the cell at which to calculate
	threshold	the threshold above which the depolarisations are counted

Definition at line 231 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetNumberOfAboveThresholdDepolarisationsForLastAp(), mTimes, and rCacheVoltages().

Member Data Documentation

Hdf5DataReader* PropagationPropertiesCalculator::mpDataReader [private]

Reader to get the data from which we use to calculate properties.

Definition at line 48 of file PropagationPropertiesCalculator.hpp.

Referenced by CalculateAllConductionVelocities(), CalculateConductionVelocity(), and rCacheVoltages().

const std::string PropagationPropertiesCalculator::mVoltageName [private]

Name of the variable representing the membrane potential.

Definition at line 50 of file PropagationPropertiesCalculator.hpp.

Referenced by CalculateAllConductionVelocities(), CalculateConductionVelocity(), and rCacheVoltages().

std::vector<double> PropagationPropertiesCalculator::mTimes [private]

Time values

Definition at line 52 of file PropagationPropertiesCalculator.hpp.

Referenced by CalculateAboveThresholdDepolarisationsForLastAp(), CalculateActionPotentialDuration(), CalculateAllAboveThresholdDepolarisations(), CalculateAllActionPotentialDurations(), CalculateAllConductionVelocities(), CalculateAllMaximumUpstrokeVelocities(), CalculateConductionVelocity(), CalculateMaximumUpstrokeVelocity(), and CalculateUpstrokeTimes().

unsigned PropagationPropertiesCalculator::mCachedNodeGlobalIndex [private]

Which node voltages have been cached for, if any

Definition at line 54 of file PropagationPropertiesCalculator.hpp.

Referenced by rCacheVoltages().

std::vector<double> PropagationPropertiesCalculator::mCachedVoltages [private]

The cached voltages vector

Definition at line 56 of file PropagationPropertiesCalculator.hpp.

Referenced by rCacheVoltages().

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

heart/src/postprocessing/PropagationPropertiesCalculator.hpp
heart/src/postprocessing/PropagationPropertiesCalculator.cpp


Public Member Functions
	PropagationPropertiesCalculator (Hdf5DataReader *pDataReader, const std::string voltageName="V")
double	CalculateMaximumUpstrokeVelocity (unsigned globalNodeIndex)
std::vector< double >	CalculateAllMaximumUpstrokeVelocities (unsigned globalNodeIndex, double threshold)
std::vector< double >	CalculateUpstrokeTimes (unsigned globalNodeIndex, double threshold)
double	CalculateConductionVelocity (unsigned globalNearNodeIndex, unsigned globalFarNodeIndex, const double euclideanDistance)
std::vector< double >	CalculateAllConductionVelocities (unsigned globalNearNodeIndex, unsigned globalFarNodeIndex, const double euclideanDistance)
double	CalculateActionPotentialDuration (const double percentage, unsigned globalNodeIndex)
double	CalculatePeakMembranePotential (unsigned globalNodeIndex)
std::vector< double >	CalculateAllActionPotentialDurations (const double percentage, unsigned globalNodeIndex, double threshold)
std::vector< unsigned >	CalculateAllAboveThresholdDepolarisations (unsigned globalNodeIndex, double threshold)
unsigned	CalculateAboveThresholdDepolarisationsForLastAp (unsigned globalNodeIndex, double threshold)
Private Member Functions
std::vector< double > &	rCacheVoltages (unsigned globalNodeIndex)
Private Attributes
Hdf5DataReader *	mpDataReader
const std::string	mVoltageName
std::vector< double >	mTimes
unsigned	mCachedNodeGlobalIndex
std::vector< double >	mCachedVoltages