PropagationPropertiesCalculator Class Reference

#include <PropagationPropertiesCalculator.hpp>

Collaboration diagram for PropagationPropertiesCalculator:

Public Member Functions
	PropagationPropertiesCalculator (Hdf5DataReader *pDataReader, const std::string voltageName="V")
virtual	~PropagationPropertiesCalculator ()
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< std::vector < double > >	CalculateAllActionPotentialDurationsForNodeRange (const double percentage, unsigned lowerNodeIndex, unsigned upperNodeIndex, double threshold)
std::vector< unsigned >	CalculateAllAboveThresholdDepolarisations (unsigned globalNodeIndex, double threshold)
unsigned	CalculateAboveThresholdDepolarisationsForLastAp (unsigned globalNodeIndex, double threshold)
void	SetHdf5DataReader (Hdf5DataReader *pDataReader)
Protected Member Functions
std::vector< double > &	rGetCachedVoltages (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 (node)
(all) action potential durations for a range of nodes
maximum transmembrane potential (maximum systolic potential) at a single cell.

Definition at line 53 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 43 of file PropagationPropertiesCalculator.cpp.

PropagationPropertiesCalculator::~PropagationPropertiesCalculator ( ) [virtual]

Destructor

Definition at line 51 of file PropagationPropertiesCalculator.cpp.

Member Function Documentation

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

Returns:: 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 300 of file PropagationPropertiesCalculator.cpp.

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

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

Returns:: 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 77 of file PropagationPropertiesCalculator.cpp.

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

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

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

Returns:: 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 292 of file PropagationPropertiesCalculator.cpp.

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

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

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

Returns:: 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 89 of file PropagationPropertiesCalculator.cpp.

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

std::vector< std::vector< double > > PropagationPropertiesCalculator::CalculateAllActionPotentialDurationsForNodeRange	(	const double	percentage,
		unsigned	lowerNodeIndex,
		unsigned	upperNodeIndex,
		double	threshold
	)

Returns:: all the action potentials duration at cells [lowerNodeIndex, upperNodeIndex-1].

Parameters:

	percentage	The percentage of the amplitude to calculate for.
	lowerNodeIndex	First cell at which to calculate.
	upperNodeIndex	One past the last cell at which to calculate.
	threshold	The voltage threshold for APD calculation (we count this as the start of an AP)

Definition at line 98 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetAllActionPotentialDurations(), Exception::GetShortMessage(), Hdf5DataReader::GetVariableOverTimeOverMultipleNodes(), mpDataReader, mTimes, and mVoltageName.

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

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

Returns:: 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.

Todo:: remove magic number? (#1884)

Definition at line 227 of file PropagationPropertiesCalculator.cpp.

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

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

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

Returns:: 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 63 of file PropagationPropertiesCalculator.cpp.

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

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

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

Returns:: 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.

Todo:: remove magic number? (#1884)

Definition at line 171 of file PropagationPropertiesCalculator.cpp.

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

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

double PropagationPropertiesCalculator::CalculateMaximumUpstrokeVelocity ( unsigned globalNodeIndex )

Returns:: 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 56 of file PropagationPropertiesCalculator.cpp.

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

double PropagationPropertiesCalculator::CalculatePeakMembranePotential ( unsigned globalNodeIndex )

Returns:: 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 157 of file PropagationPropertiesCalculator.cpp.

References rGetCachedVoltages().

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

Returns:: 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 70 of file PropagationPropertiesCalculator.cpp.

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

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

std::vector< double > & PropagationPropertiesCalculator::rGetCachedVoltages ( unsigned globalNodeIndex ) [protected]

Returns:: 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 308 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().