PropagationPropertiesCalculator Class Reference

#include <PropagationPropertiesCalculator.hpp>

Collaboration diagram for PropagationPropertiesCalculator:

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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 Attributes

Hdf5DataReader * mpDataReader
const std::string mVoltageName

Detailed Description

Calculate physiological properties at given global mesh indices

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

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 46 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetLastMaxUpstrokeVelocity(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableOverTime(), mpDataReader, and mVoltageName.

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 54 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetMaxUpstrokeVelocities(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableOverTime(), mpDataReader, and mVoltageName.

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(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableOverTime(), mpDataReader, and mVoltageName.

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 106 of file PropagationPropertiesCalculator.cpp.

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

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 162 of file PropagationPropertiesCalculator.cpp.

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

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 70 of file PropagationPropertiesCalculator.cpp.

References EXCEPTION, CellProperties::GetLastActionPotentialDuration(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableOverTime(), mpDataReader, and mVoltageName.

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 92 of file PropagationPropertiesCalculator.cpp.

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

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 83 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetAllActionPotentialDurations(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableOverTime(), mpDataReader, and mVoltageName.

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 226 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetNumberOfAboveThresholdDepolarisationsForAllAps(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableOverTime(), mpDataReader, and mVoltageName.

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 235 of file PropagationPropertiesCalculator.cpp.

References CellProperties::GetNumberOfAboveThresholdDepolarisationsForLastAp(), Hdf5DataReader::GetUnlimitedDimensionValues(), Hdf5DataReader::GetVariableOverTime(), mpDataReader, and mVoltageName.

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

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

Name of the variable representing the membrane potential.

Definition at line 50 of file PropagationPropertiesCalculator.hpp.

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

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