Typedefs
typedef std::unordered_set< ID >	neighbors_Type

typedef std::vector< neighbors_Type >	neighborList_Type

Methods
HeartUtility Author (s) Simone Rossi `HeartUtility` contains methods for reading vectorial data from different formats to VectorEpetra objects.
typedef std::function< Real(const Real &t, const Real &x, const Real &y, const Real &z, const ID &i) >	function_Type

template<typename Mesh >
void	appliedCurrentClosestPointWithinRadius (std::vector< Real > &point, Real Radius, std::shared_ptr< VectorEpetra > appliedCurrentVector, Real valueAppliedCurrent, std::shared_ptr< Mesh > fullMesh, std::shared_ptr< Epetra_Comm > Comm)
	Find closest point within radius and applied a constant current. More...

template<typename Mesh >
void	appliedCurrentPointsWithinRadius (std::vector< Real > &point, Real Radius, std::shared_ptr< VectorEpetra > appliedCurrentVector, Real valueAppliedCurrent, std::shared_ptr< Mesh > fullMesh)
	Find all the points within radius and applied a constant current. More...

template<typename Mesh >
UInt	findClosestPoint (std::vector< Real > &point, std::shared_ptr< VectorEpetra > vec, std::shared_ptr< Mesh > fullMesh, std::shared_ptr< Epetra_Comm > Comm)
	Find closest point to a given one in the mesh. More...

template<typename Mesh >
void	allIdsPointsWithGivenFlag (std::vector< ID > &containerIds, UInt flag, std::shared_ptr< VectorEpetra > vec, std::shared_ptr< Mesh > fullMesh)
	Collect all the ids of points with a given flag in a local vector for each processor. More...

template<typename Type >
Type	randomPointInSet (std::vector< Type > &container)
	Select randomly a value in a given set and update the set by deleting the chosen value from the set. More...

void	randomPointInSetAndNeighborhood (std::vector< ID > &container, std::vector< ID > &selectedPoints, neighborList_Type &neighbors)
	Select randomly a point in a given set and its neighborhood and update the set by deleting the chosen value from the set. More...

template<typename Type >
void	randomNPointsInSet (std::vector< Type > &container, std::vector< Type > &selectedValue, UInt N)
	Select randomly N values in a given set and update the set by deleting the chosen N values from the set. More...

template<typename Mesh >
void	randomNPointsInSetAndNeighborhood (std::vector< ID > &container, std::vector< ID > &selectedValue, std::vector< Real > &activationTime, Real deltaT, UInt N, Mesh &fullMesh, std::shared_ptr< Epetra_Comm > Comm)
	Select randomly N values in a given set and update the set by deleting the chosen N values from the set. More...

template<typename Type >
void	applyCurrentGivenSetOfPoints (std::vector< Type > &container, std::shared_ptr< VectorEpetra > appliedCurrentVector, Real valueAppliedCurrent)
	Apply given current to a set of points. More...

template<typename Type >
void	applyCurrentGivenSetOfPoints (std::vector< Type > &container, std::vector< Real > activationTime, std::shared_ptr< VectorEpetra > appliedCurrentVector, std::vector< Real > &valueAppliedCurrent, std::vector< UInt > &shiftVector, Real currentTime)
	Apply given current with a set of PMJs. More...

template<typename Mesh >
void	importFibers (std::shared_ptr< VectorEpetra > fiberVector, const std::string &fileName, std::shared_ptr< Mesh > localMesh, const std::string &filePath="./")
	Read fiber vector field from HDF5 file. More...

template<typename Mesh >
void	importScalarField (std::shared_ptr< VectorEpetra > vector, const std::string &fileName, const std::string &fieldName, std::shared_ptr< Mesh > localMesh)
	Read scalar field from HDF5 file. More...

template<typename Mesh >
void	importVectorField (std::shared_ptr< VectorEpetra > vector, const std::string &fileName, const std::string &fieldName, std::shared_ptr< Mesh > localMesh, const std::string &postDir="./")
	Read vector field from HDF5 file. More...

void	importFibersFromTextFile (std::shared_ptr< VectorEpetra > fiberVector, std::string fileName, std::string filePath, int format=0)
	Read fiber field from text file. More...

void	setupFibers (VectorEpetra &fiberVector, VectorSmall< 3 > &fiberDirection)
	Setup fiber field from unidirectional VectorSmall object. More...

void	setupFibers (VectorEpetra &fiberVector, std::vector< Real > &fiberDirection)
	Setup fiber field from unidirectional std::vector object. More...

void	setupFibers (VectorEpetra &fiberVector, Real fx, Real fy, Real fz)
	Setup fiber field from three real components. More...

void	setValueOnBoundary (VectorEpetra &vec, std::shared_ptr< RegionMesh< LinearTetra > > fullMesh, Real value, UInt flag)
	On the boundary with the specified flag, set the wanted value. More...

void	setValueOnBoundary (VectorEpetra &vec, std::shared_ptr< RegionMesh< LinearTetra > > fullMesh, Real value, std::vector< UInt > flags)
	On the boundary with the specified flags, set the wanted value. More...

void	rescaleVector (VectorEpetra &vector, Real minValue, Real maxValue, Real scaleFactor=1.0)
	Rescale a scalar field to be between requested bounds. More...

void	rescaleVector (VectorEpetra &vector, Real scaleFactor=1.0)
	Rescale a scalar field by a constant factor. More...

void	rescaleVectorOnBoundary (VectorEpetra &vector, std::shared_ptr< RegionMesh< LinearTetra > > fullMesh, UInt flag, Real scaleFactor=1.0)
	Rescale a scalar field by a constant factor on a boundary. More...

void	normalize (VectorEpetra &vector)
	Normalizes a vector field to unit length. More...

void	addNoiseToFibers (VectorEpetra &fiberVector, Real magnitude=0.01, std::vector< bool > component=std::vector< bool >(3, true))
	Add random component to the fibers. More...

template<typename Mesh >
void	setFibersFromFunction (std::shared_ptr< VectorEpetra > vector, std::shared_ptr< Mesh > localMesh, function_Type f)

Typedef Documentation

◆ neighbors_Type

typedef std::unordered_set<ID> neighbors_Type

Definition at line 64 of file ElectrophysiologyUtility.hpp.

◆ neighborList_Type

typedef std::vector<neighbors_Type> neighborList_Type

Definition at line 65 of file ElectrophysiologyUtility.hpp.

◆ function_Type

typedef std::function< Real (const Real& t, const Real& x, const Real& y, const Real& z, const ID& i ) > function_Type

Definition at line 481 of file HeartUtility.hpp.

Function Documentation

◆ appliedCurrentClosestPointWithinRadius()

void LifeV::ElectrophysiologyUtility::appliedCurrentClosestPointWithinRadius	(	std::vector< Real > &	point,
		Real	Radius,
		std::shared_ptr< VectorEpetra >	appliedCurrentVector,
		Real	valueAppliedCurrent,
		std::shared_ptr< Mesh >	fullMesh,
		std::shared_ptr< Epetra_Comm >	Comm
	)

inline

Find closest point within radius and applied a constant current.

Parameters

point	Vector of real containing the coordinates of the point within the radius
radius	Radius used to find point.
appliedCurrentVector	Vector epetra containing the applied current.
valueAppliedCurrent	Value of the current to apply at the specified point.
fullMesh	Pointer to the mesh.
Comm	EpetraMpi comunicator.

Definition at line 87 of file ElectrophysiologyUtility.hpp.

◆ appliedCurrentPointsWithinRadius()

void LifeV::ElectrophysiologyUtility::appliedCurrentPointsWithinRadius	(	std::vector< Real > &	point,
		Real	Radius,
		std::shared_ptr< VectorEpetra >	appliedCurrentVector,
		Real	valueAppliedCurrent,
		std::shared_ptr< Mesh >	fullMesh
	)

inline

Find all the points within radius and applied a constant current.

Parameters

point	Vector of real containing the coordinates of the point within the radius
radius	Radius used to find point.
appliedCurrentVector	Vector epetra containing the applied current.
valueAppliedCurrent	Value of the current to apply at the specified point.
fullMesh	Pointer to the mesh.

Definition at line 130 of file ElectrophysiologyUtility.hpp.

◆ findClosestPoint()

UInt LifeV::ElectrophysiologyUtility::findClosestPoint	(	std::vector< Real > &	point,
		std::shared_ptr< VectorEpetra >	vec,
		std::shared_ptr< Mesh >	fullMesh,
		std::shared_ptr< Epetra_Comm >	Comm
	)

inline

Find closest point to a given one in the mesh.

Parameters

point	Vector of real containing the coordinates of the point within the radius
vec	Vector epetra used to recover Global id.
fullMesh	Pointer to the mesh.
Comm	EpetraMpi comunicator.

Returns: The ids of the closest point

Definition at line 167 of file ElectrophysiologyUtility.hpp.

◆ allIdsPointsWithGivenFlag()

void LifeV::ElectrophysiologyUtility::allIdsPointsWithGivenFlag	(	std::vector< ID > &	containerIds,
		UInt	flag,
		std::shared_ptr< VectorEpetra >	vec,
		std::shared_ptr< Mesh >	fullMesh
	)

inline

Collect all the ids of points with a given flag in a local vector for each processor.

Parameters

containerIds	Vector containig all the ids of the points with a given flag
flag	Flag.
vec	Vector epetra used to recover Global id.
fullMesh	Pointer to the mesh.

Definition at line 212 of file ElectrophysiologyUtility.hpp.

◆ randomPointInSet()

Type LifeV::ElectrophysiologyUtility::randomPointInSet ( std::vector< Type > & container )

inline

Select randomly a value in a given set and update the set by deleting the chosen value from the set.

Parameters

container vector containig all the value

Returns: Selected value

Definition at line 228 of file ElectrophysiologyUtility.hpp.

◆ randomPointInSetAndNeighborhood()

void LifeV::ElectrophysiologyUtility::randomPointInSetAndNeighborhood	(	std::vector< ID > &	container,
		std::vector< ID > &	selectedPoints,
		neighborList_Type &	neighbors
	)

inline

Select randomly a point in a given set and its neighborhood and update the set by deleting the chosen value from the set.

Parameters

container	vector containig all the value
selectedPoints	selected points
neighbors	cointainer of the neighbors

Definition at line 244 of file ElectrophysiologyUtility.hpp.

◆ randomNPointsInSet()

void LifeV::ElectrophysiologyUtility::randomNPointsInSet	(	std::vector< Type > &	container,
		std::vector< Type > &	selectedValue,
		UInt	N
	)

inline

Select randomly N values in a given set and update the set by deleting the chosen N values from the set.

Parameters

container	Set containig all the value
selectedValue	vector containg the selected values
N	number of values we want to select

Definition at line 266 of file ElectrophysiologyUtility.hpp.

◆ randomNPointsInSetAndNeighborhood()

void LifeV::ElectrophysiologyUtility::randomNPointsInSetAndNeighborhood	(	std::vector< ID > &	container,
		std::vector< ID > &	selectedValue,
		std::vector< Real > &	activationTime,
		Real	deltaT,
		UInt	N,
		Mesh &	fullMesh,
		std::shared_ptr< Epetra_Comm >	Comm
	)

inline

Select randomly N values in a given set and update the set by deleting the chosen N values from the set.

Parameters

container	Set containig all the value
selectedValue	vector containg the selected values
N	number of values we want to select
fullMesh	mesh used to determine the neighborhood

Definition at line 283 of file ElectrophysiologyUtility.hpp.

◆ applyCurrentGivenSetOfPoints() [1/2]

void LifeV::ElectrophysiologyUtility::applyCurrentGivenSetOfPoints	(	std::vector< Type > &	container,
		std::shared_ptr< VectorEpetra >	appliedCurrentVector,
		Real	valueAppliedCurrent
	)

inline

Apply given current to a set of points.

Parameters

container	Set containig all the globalIDs of points to which we want to apply the current
appliedCurrentVector	vector containg the current
valueAppliedCurrent	value of the current we want to apply

Definition at line 310 of file ElectrophysiologyUtility.hpp.

◆ applyCurrentGivenSetOfPoints() [2/2]

void LifeV::ElectrophysiologyUtility::applyCurrentGivenSetOfPoints	(	std::vector< Type > &	container,
		std::vector< Real >	activationTime,
		std::shared_ptr< VectorEpetra >	appliedCurrentVector,
		std::vector< Real > &	valueAppliedCurrent,
		std::vector< UInt > &	shiftVector,
		Real	currentTime
	)

inline

Apply given current with a set of PMJs.

Parameters

container	vector containig all the globalIDs of the PMJs to which we want to apply the current
timeActivation	vector containig the activation time of the PMJs
appliedCurrentVector	vector containg the applied current
valueAppliedCurrent	vector containig the apply current during the all simulation time
shiftVector	vector containig the index that refers to the value of applied current in each PMJ
currentTime	current time

Definition at line 332 of file ElectrophysiologyUtility.hpp.

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◆ importFibers()

void LifeV::ElectrophysiologyUtility::importFibers	(	std::shared_ptr< VectorEpetra >	fiberVector,
		const std::string &	fileName,
		std::shared_ptr< Mesh >	localMesh,
		const std::string &	filePath = `"./"`
	)

inline

Read fiber vector field from HDF5 file.

Parameters

fiberVector	VectorEpetra object for storing the vector field
fileName	Name of the HDF5 file to read from
localMesh	Pointer to the mesh

Definition at line 78 of file HeartUtility.hpp.

◆ importScalarField()

void LifeV::ElectrophysiologyUtility::importScalarField	(	std::shared_ptr< VectorEpetra >	vector,
		const std::string &	fileName,
		const std::string &	fieldName,
		std::shared_ptr< Mesh >	localMesh
	)

inline

Read scalar field from HDF5 file.

Parameters

vector	VectorEpetra object for storing the scalar field
fileName	Name of the HDF5 file to read from
fieldName	Name of the scalar field in the HDF5 file
localMesh	Pointer to the mesh

Definition at line 109 of file HeartUtility.hpp.

◆ importVectorField()

void LifeV::ElectrophysiologyUtility::importVectorField	(	std::shared_ptr< VectorEpetra >	vector,
		const std::string &	fileName,
		const std::string &	fieldName,
		std::shared_ptr< Mesh >	localMesh,
		const std::string &	postDir = `"./"`
	)

inline

Read vector field from HDF5 file.

Parameters

vector	VectorEpetra object for storing the scalar field
fileName	Name of the HDF5 file to read from
fieldName	Name of the vector field in the HDF5 file
localMesh	Pointer to the mesh

Definition at line 139 of file HeartUtility.hpp.

◆ importFibersFromTextFile()

void LifeV::ElectrophysiologyUtility::importFibersFromTextFile	(	std::shared_ptr< VectorEpetra >	fiberVector,
		std::string	fileName,
		std::string	filePath,
		int	format = `0`
	)

inline

Read fiber field from text file.

Parameters

fiberVector	VectorEpetra object for storing the vector field
fileName	Name of the HDF5 file to read from
filePath	Path of the HDF5 file to read from
format	The fibers can be in the text file in two different formats:

format 0 = fibers saved as (fx, fy, fz) in each row

format 1 = fibers saved as fx in each row for all the mesh fy in each row for all the mesh fz in each row for all the mesh

Definition at line 176 of file HeartUtility.hpp.

◆ setupFibers() [1/3]

void LifeV::ElectrophysiologyUtility::setupFibers	(	VectorEpetra &	fiberVector,
		VectorSmall< 3 > &	fiberDirection
	)

inline

Setup fiber field from unidirectional VectorSmall object.

Parameters

fiberVector	VectorEpetra object for storing the vector field
fiberDirection	Direction of fiber vectors as a VectorSmall

Definition at line 258 of file HeartUtility.hpp.

◆ setupFibers() [2/3]

void LifeV::ElectrophysiologyUtility::setupFibers	(	VectorEpetra &	fiberVector,
		std::vector< Real > &	fiberDirection
	)

inline

Setup fiber field from unidirectional std::vector object.

Parameters

fiberVector	VectorEpetra object for storing the vector field
fiberDirection	Direction of fiber vectors as a VectorSmall

Definition at line 284 of file HeartUtility.hpp.

◆ setupFibers() [3/3]

void LifeV::ElectrophysiologyUtility::setupFibers	(	VectorEpetra &	fiberVector,
		Real	fx,
		Real	fy,
		Real	fz
	)

inline

Setup fiber field from three real components.

Parameters

fiberVector	VectorEpetra object for storing the vector field
fx	First component of vector
fy	Second component of vector
fz	Third component of vector

Definition at line 300 of file HeartUtility.hpp.

◆ setValueOnBoundary() [1/2]

void LifeV::ElectrophysiologyUtility::setValueOnBoundary	(	VectorEpetra &	vec,
		std::shared_ptr< RegionMesh< LinearTetra > >	fullMesh,
		Real	value,
		UInt	flag
	)

inline

On the boundary with the specified flag, set the wanted value.

Parameters

vec	VectorEpetra object where we want to impose the boundary value
fullMesh	Pointer to the non partitioned mesh
value	value to set on that boundary
flag	flag of the boundary

Definition at line 317 of file HeartUtility.hpp.

◆ setValueOnBoundary() [2/2]

void LifeV::ElectrophysiologyUtility::setValueOnBoundary	(	VectorEpetra &	vec,
		std::shared_ptr< RegionMesh< LinearTetra > >	fullMesh,
		Real	value,
		std::vector< UInt >	flags
	)

inline

On the boundary with the specified flags, set the wanted value.

Parameters

vec	VectorEpetra object where we want to impose the boundary value
fullMesh	Pointer to the non partitioned mesh
value	value to set on that boundary
flags	flags of the boundary

Definition at line 340 of file HeartUtility.hpp.

◆ rescaleVector() [1/2]

void LifeV::ElectrophysiologyUtility::rescaleVector	(	VectorEpetra &	vector,
		Real	minValue,
		Real	maxValue,
		Real	scaleFactor = `1.0`
	)

inline

Rescale a scalar field to be between requested bounds.

Parameters

vector	VectorEpetra object that contains the scalar field
minValue	Minimum value
maxValue	Maximum value
scaleFactor	Additional scaling factor (defaults to 1)

Definition at line 364 of file HeartUtility.hpp.

◆ rescaleVector() [2/2]

void LifeV::ElectrophysiologyUtility::rescaleVector	(	VectorEpetra &	vector,
		Real	scaleFactor = `1.0`
	)

inline

Rescale a scalar field by a constant factor.

Parameters

vector	VectorEpetra object that contains the scalar field
scaleFactor	Additional scaling factor (defaults to 1)

Definition at line 375 of file HeartUtility.hpp.

◆ rescaleVectorOnBoundary()

void LifeV::ElectrophysiologyUtility::rescaleVectorOnBoundary	(	VectorEpetra &	vector,
		std::shared_ptr< RegionMesh< LinearTetra > >	fullMesh,
		UInt	flag,
		Real	scaleFactor = `1.0`
	)

inline

Rescale a scalar field by a constant factor on a boundary.

Parameters

vector	VectorEpetra object that contains the scalar field
fullMesh	pointer to the non partitioned mesh
flag	flag of the boundary
scaleFactor	Additional scaling factor (defaults to 1)

Definition at line 389 of file HeartUtility.hpp.

◆ normalize()

void LifeV::ElectrophysiologyUtility::normalize ( VectorEpetra & vector )

inline

Normalizes a vector field to unit length.

Parameters

vector VectorEpetra object that contains the vector field

Definition at line 407 of file HeartUtility.hpp.

◆ addNoiseToFibers()

void LifeV::ElectrophysiologyUtility::addNoiseToFibers	(	VectorEpetra &	fiberVector,
		Real	magnitude = `0.01`,
		std::vector< bool >	component = `std::vector<bool> (3, true)`
	)

inline

Add random component to the fibers.

Parameters

fiberVector	VectorEpetra object for storing the vector field
fiberDirection	Direction of fiber vectors as a VectorSmall

Definition at line 445 of file HeartUtility.hpp.

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◆ setFibersFromFunction()

void LifeV::ElectrophysiologyUtility::setFibersFromFunction	(	std::shared_ptr< VectorEpetra >	vector,
		std::shared_ptr< Mesh >	localMesh,
		function_Type	f
	)

inline

Definition at line 482 of file HeartUtility.hpp.

Typedefs

Methods

Typedef Documentation

◆ neighbors_Type

◆ neighborList_Type

◆ function_Type

Function Documentation

◆ appliedCurrentClosestPointWithinRadius()

◆ appliedCurrentPointsWithinRadius()

◆ findClosestPoint()

◆ allIdsPointsWithGivenFlag()

◆ randomPointInSet()

◆ randomPointInSetAndNeighborhood()

◆ randomNPointsInSet()

◆ randomNPointsInSetAndNeighborhood()

◆ applyCurrentGivenSetOfPoints() [1/2]

◆ applyCurrentGivenSetOfPoints() [2/2]

◆ importFibers()

◆ importScalarField()

◆ importVectorField()

◆ importFibersFromTextFile()

◆ setupFibers() [1/3]

◆ setupFibers() [2/3]

◆ setupFibers() [3/3]

◆ setValueOnBoundary() [1/2]

◆ setValueOnBoundary() [2/2]

◆ rescaleVector() [1/2]

◆ rescaleVector() [2/2]

◆ rescaleVectorOnBoundary()

◆ normalize()

◆ addNoiseToFibers()

◆ setFibersFromFunction()