CEPS: ActivationTracker Class Reference

Detailed Description

Class managing computations from potential to outputs.

Not only this class outputs the solution vector (one scalar field per component), it also handles the computation of activation times.

Activation times are defined by $t_\mathrm{activ}(v_\mathrm{th},\bm{x}) = \min \max_{t>t_\mathrm{start}} \{t | V(t,\bm{x}) > v_\mathrm{th}\}$ Depolarization times are defined by $t_\mathrm{depol}(v_\mathrm{th},\bm{x}) = \min \max_{t>t_\mathrm{start}} \{t | V(t,\bm{x}) < v_\mathrm{th}\}$ where is a depolarization threshold than can be set multiple times.

AP peaks are detected as the first time the AP decreases after activation time.

Definition at line 59 of file ActivationTracker.hpp.

#include <ActivationTracker.hpp>

Inheritance diagram for ActivationTracker:

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Public Member Functions
	ActivationTracker (CardiacSolver *solver)
	Constructor. More...

	~ActivationTracker ()
	Destructor. More...

void	update (CepsInt iter, CepsReal time, DHVecPtr solution, DHVecPtr prevSolution)
	Writes the solution (optionnally currents) every m_nbIterSnapshot steps only. Also updates activation times. More...

void	writeActivationMap ()
	Writes activation times and probe points data. More...

CepsBool	allPointsHaveBeenActivated () const
	Tells if all points have seen AP start (checked with activation threshold) More...

CepsBool	allPointsHaveBeenRepolarized () const
	Tells if all points have seen AP end (checked with APD percentage) More...

CepsString	getByeByeMessage () const
	Message to be displayed at the end of computation. More...

CepsVector< CepsReal > &	getActivatedVolume ()
	Returns reference to data, so it can be linked to a TimeWriter. More...

Public Member Functions inherited from CepsObject
	CepsObject ()=default
	default constructor More...

	CepsObject (const CepsObject &)=default
	Copy constructor. More...

virtual	~CepsObject ()=default
	Destructor. More...

CepsObject &	operator= (const CepsObject &)=default
	Assignment operator. More...

CepsObject *	toBaseObject ()
	Returns a pointer to CepsObject class. More...

const CepsObject *	toBaseObject () const
	Returns a pointer to CepsObject class, const version. More...

Profiler *	getProfiler () const
	Access to profiler. More...

Protected Member Functions
void	setupWithParameters (InputParameters *params)
	Initializes attributes from text input. More...

void	initializeActivationMap ()
	Allocates arrays for activation detection. More...

CepsBool	allSeen (const CepsMap< CepsUnknownIndex, CepsSet< CepsDofGlobalIndex >> &) const
	Check not nans for given array. More...

Protected Attributes
CardiacProblem *	m_problem
	Link to problem structure. More...

Geometry *	m_geom
	Geometry. More...

TimeWriter *	m_timeWriter
	Link to the solver's time writer, if needed... More...

CepsUInt	m_nbIterPostProcess
	Output periodicity. More...

CepsMap< CepsUnknownIndex, CepsReal3D >	m_activationTimeData
	AP analysis. More...

DHVecPtr	m_activationTimes
	Values of activation times at each point. More...

DHVecPtr	m_activated
	1/0 status of point (above/below threshold) More...

DHVecPtr	m_peakValues
	Value of max potential. More...

DHVecPtr	m_peakTimes
	Times of max potential. More...

DHVecPtr	m_APD50
	length of AP to get to 50% depol More...

DHVecPtr	m_APD
	length of AP (?) More...

CepsMap< CepsUnknownIndex, CepsSet< CepsDofGlobalIndex > >	m_activationNotYetSeen
	Flag map. More...

CepsMap< CepsUnknownIndex, CepsSet< CepsDofGlobalIndex > >	m_activationSeen
	Flag map. More...

CepsMap< CepsUnknownIndex, CepsSet< CepsDofGlobalIndex > >	m_foundPeak
	Flag map. More...

CepsMap< CepsUnknownIndex, CepsSet< CepsDofGlobalIndex > >	m_foundAPD50
	Flag map. More...

CepsMap< CepsUnknownIndex, CepsSet< CepsDofGlobalIndex > >	m_foundAPD
	Flag map. More...

CepsVector< CepsReal >	m_activatedVolume
	Size of tissue that is above activation threshold. More...

CepsReal	m_tissueVolume
	Reference volume. More...

CepsUInt	m_nToBeSeen
	Number of dofs in tissue for each activation time data. More...

Static Protected Attributes
static constexpr CepsUInt	_threshold = 0
	Index in activation data. More...

static constexpr CepsUInt	_apdpctg = 1
	Index in activation data. More...

static constexpr CepsUInt	_minV4Peak = 2
	Index in activation data. More...

Static Protected Attributes inherited from CepsObject
static Profiler	m_profiler
	The same profiler for each big object. More...

Constructor & Destructor Documentation

◆ ActivationTracker()

ActivationTracker::ActivationTracker ( CardiacSolver * solver )

Constructor.

Parameters

[in] solver link to CardiacSolver structure

Definition at line 36 of file ActivationTracker.cpp.

◆ ~ActivationTracker()

ActivationTracker::~ActivationTracker ( )

Destructor.

Definition at line 67 of file ActivationTracker.cpp.

Member Function Documentation

◆ allPointsHaveBeenActivated()

CepsBool ActivationTracker::allPointsHaveBeenActivated ( ) const

Tells if all points have seen AP start (checked with activation threshold)

Definition at line 231 of file ActivationTracker.cpp.

◆ allPointsHaveBeenRepolarized()

CepsBool ActivationTracker::allPointsHaveBeenRepolarized ( ) const

Tells if all points have seen AP end (checked with APD percentage)

Definition at line 239 of file ActivationTracker.cpp.

◆ allSeen()

CepsBool ActivationTracker::allSeen ( const CepsMap< CepsUnknownIndex, CepsSet< CepsDofGlobalIndex >> & arrays ) const

protected

Check not nans for given array.

Definition at line 357 of file ActivationTracker.cpp.

◆ getActivatedVolume()

CepsVector< CepsReal > & ActivationTracker::getActivatedVolume ( )

Returns reference to data, so it can be linked to a TimeWriter.

Definition at line 253 of file ActivationTracker.cpp.

◆ getByeByeMessage()

CepsString ActivationTracker::getByeByeMessage ( ) const

Message to be displayed at the end of computation.

Definition at line 247 of file ActivationTracker.cpp.

◆ initializeActivationMap()

void ActivationTracker::initializeActivationMap ( )

protected

Allocates arrays for activation detection.

Definition at line 286 of file ActivationTracker.cpp.

◆ setupWithParameters()

void ActivationTracker::setupWithParameters ( InputParameters * params )

protected

Initializes attributes from text input.

Definition at line 259 of file ActivationTracker.cpp.

◆ update()

void ActivationTracker::update	(	CepsInt	iter,
		CepsReal	time,
		DHVecPtr	solution,
		DHVecPtr	prevSolution
	)

Writes the solution (optionnally currents) every m_nbIterSnapshot steps only. Also updates activation times.

Definition at line 75 of file ActivationTracker.cpp.

◆ writeActivationMap()

void ActivationTracker::writeActivationMap ( )

Writes activation times and probe points data.

Definition at line 193 of file ActivationTracker.cpp.

Field Documentation

◆ _apdpctg

constexpr CepsUInt ActivationTracker::_apdpctg = 1

staticconstexprprotected

Index in activation data.

Definition at line 121 of file ActivationTracker.hpp.

◆ _minV4Peak

constexpr CepsUInt ActivationTracker::_minV4Peak = 2

staticconstexprprotected

Index in activation data.

Definition at line 122 of file ActivationTracker.hpp.

◆ _threshold

constexpr CepsUInt ActivationTracker::_threshold = 0

staticconstexprprotected

Index in activation data.

Definition at line 120 of file ActivationTracker.hpp.

◆ m_activated

DHVecPtr ActivationTracker::m_activated

protected

1/0 status of point (above/below threshold)

Definition at line 125 of file ActivationTracker.hpp.

◆ m_activatedVolume

CepsVector<CepsReal> ActivationTracker::m_activatedVolume

protected

Size of tissue that is above activation threshold.

Definition at line 137 of file ActivationTracker.hpp.

◆ m_activationNotYetSeen

CepsMap<CepsUnknownIndex,CepsSet<CepsDofGlobalIndex> > ActivationTracker::m_activationNotYetSeen

protected

Flag map.

Definition at line 131 of file ActivationTracker.hpp.

◆ m_activationSeen

CepsMap<CepsUnknownIndex,CepsSet<CepsDofGlobalIndex> > ActivationTracker::m_activationSeen

protected

Flag map.

Definition at line 132 of file ActivationTracker.hpp.

◆ m_activationTimeData

CepsMap<CepsUnknownIndex,CepsReal3D> ActivationTracker::m_activationTimeData

protected

AP analysis.

Definition at line 119 of file ActivationTracker.hpp.

◆ m_activationTimes

DHVecPtr ActivationTracker::m_activationTimes

protected

Values of activation times at each point.

Definition at line 124 of file ActivationTracker.hpp.

◆ m_APD

DHVecPtr ActivationTracker::m_APD

protected

length of AP (?)

Definition at line 129 of file ActivationTracker.hpp.

◆ m_APD50

DHVecPtr ActivationTracker::m_APD50

protected

length of AP to get to 50% depol

Definition at line 128 of file ActivationTracker.hpp.

◆ m_foundAPD

CepsMap<CepsUnknownIndex,CepsSet<CepsDofGlobalIndex> > ActivationTracker::m_foundAPD

protected

Flag map.

Definition at line 135 of file ActivationTracker.hpp.

◆ m_foundAPD50

CepsMap<CepsUnknownIndex,CepsSet<CepsDofGlobalIndex> > ActivationTracker::m_foundAPD50

protected

Flag map.

Definition at line 134 of file ActivationTracker.hpp.

◆ m_foundPeak

CepsMap<CepsUnknownIndex,CepsSet<CepsDofGlobalIndex> > ActivationTracker::m_foundPeak

protected

Flag map.

Definition at line 133 of file ActivationTracker.hpp.

◆ m_geom

Geometry* ActivationTracker::m_geom

protected

Geometry.

Definition at line 114 of file ActivationTracker.hpp.

◆ m_nbIterPostProcess

CepsUInt ActivationTracker::m_nbIterPostProcess

protected

Output periodicity.

Definition at line 117 of file ActivationTracker.hpp.

◆ m_nToBeSeen

CepsUInt ActivationTracker::m_nToBeSeen

protected

Number of dofs in tissue for each activation time data.

Definition at line 140 of file ActivationTracker.hpp.

◆ m_peakTimes

DHVecPtr ActivationTracker::m_peakTimes

protected

Times of max potential.

Definition at line 127 of file ActivationTracker.hpp.

◆ m_peakValues

DHVecPtr ActivationTracker::m_peakValues

protected

Value of max potential.

Definition at line 126 of file ActivationTracker.hpp.

◆ m_problem

CardiacProblem* ActivationTracker::m_problem

protected

Link to problem structure.

Definition at line 113 of file ActivationTracker.hpp.

◆ m_timeWriter

TimeWriter* ActivationTracker::m_timeWriter

protected

Link to the solver's time writer, if needed...

Definition at line 115 of file ActivationTracker.hpp.

◆ m_tissueVolume

CepsReal ActivationTracker::m_tissueVolume

protected

Reference volume.

Definition at line 138 of file ActivationTracker.hpp.

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

/builds/xxjFYZX3/0/carmen/ceps/src/cardiac/common/ActivationTracker.hpp
/builds/xxjFYZX3/0/carmen/ceps/src/cardiac/common/ActivationTracker.cpp

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Constructor & Destructor Documentation

◆ ActivationTracker()

◆ ~ActivationTracker()

Member Function Documentation

◆ allPointsHaveBeenActivated()

◆ allPointsHaveBeenRepolarized()

◆ allSeen()

◆ getActivatedVolume()

◆ getByeByeMessage()

◆ initializeActivationMap()

◆ setupWithParameters()

◆ update()

◆ writeActivationMap()

Field Documentation

◆ _apdpctg

◆ _minV4Peak

◆ _threshold

◆ m_activated

◆ m_activatedVolume

◆ m_activationNotYetSeen

◆ m_activationSeen

◆ m_activationTimeData

◆ m_activationTimes

◆ m_APD

◆ m_APD50

◆ m_foundAPD

◆ m_foundAPD50

◆ m_foundPeak

◆ m_geom

◆ m_nbIterPostProcess

◆ m_nToBeSeen

◆ m_peakTimes

◆ m_peakValues

◆ m_problem

◆ m_timeWriter

◆ m_tissueVolume