#include <FilterElectrogram.h>

Inheritance diagram for Nektar::FilterElectrogram:

Public Member Functions
	FilterElectrogram (const LibUtilities::SessionReaderSharedPtr &pSession, const std::shared_ptr< SolverUtils::EquationSystem > &pEquation, const ParamMap &pParams)
	Electrogram filter constructor. More...

	~FilterElectrogram () override
	Electrogram filter destructor. More...

Public Member Functions inherited from Nektar::SolverUtils::Filter
SOLVER_UTILS_EXPORT	Filter (const LibUtilities::SessionReaderSharedPtr &pSession, const std::shared_ptr< EquationSystem > &pEquation)

virtual SOLVER_UTILS_EXPORT	~Filter ()

SOLVER_UTILS_EXPORT void	Initialise (const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time)

SOLVER_UTILS_EXPORT void	Update (const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time)

SOLVER_UTILS_EXPORT void	Finalise (const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time)

SOLVER_UTILS_EXPORT bool	IsTimeDependent ()

Static Public Member Functions
static SolverUtils::FilterSharedPtr	create (const LibUtilities::SessionReaderSharedPtr &pSession, const std::shared_ptr< SolverUtils::EquationSystem > &pEquation, const ParamMap &pParams)
	Creates an instance of this class. More...

Static Public Attributes
static std::string	className
	Name of the class. More...

Protected Member Functions
void	v_Initialise (const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time) override
	Initialises the electrogram filter and open output file. More...

void	v_Update (const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time) override
	Compute extracellular potential at egm points at current time. More...

void	v_Finalise (const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time) override
	Finalise the electrogram filter and close output file. More...

bool	v_IsTimeDependent () override
	Filter is time-dependent and should be called at each time-step. More...

virtual void	v_Initialise (const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time)=0

virtual void	v_Update (const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time)=0

virtual void	v_Finalise (const Array< OneD, const MultiRegions::ExpListSharedPtr > &pFields, const NekDouble &time)=0

virtual bool	v_IsTimeDependent ()=0

Private Attributes
Array< OneD, Array< OneD, NekDouble > >	m_grad_R_x
	Gradient of the radius from each electrogram point in x-direction. More...

Array< OneD, Array< OneD, NekDouble > >	m_grad_R_y
	Gradient of the radius from each electrogram point in y-direction. More...

Array< OneD, Array< OneD, NekDouble > >	m_grad_R_z
	Gradient of the radius from each electrogram point in z-direction. More...

SpatialDomains::PointGeomVector	m_electrogramPoints
	List of electrogram points. More...

unsigned int	m_index
	Counts number of calls to update (number of timesteps) More...

unsigned int	m_outputFrequency
	Number of timesteps between outputs. More...

std::string	m_outputFile
	Filename to output electrogram data to. More...

std::ofstream	m_outputStream
	Output file stream for electrogram data. More...

std::stringstream	m_electrogramStream
	Point coordinate input string. More...

Friends
class	MemoryManager< FilterElectrogram >

Additional Inherited Members
Public Types inherited from Nektar::SolverUtils::Filter
typedef std::map< std::string, std::string >	ParamMap

Protected Attributes inherited from Nektar::SolverUtils::Filter
LibUtilities::SessionReaderSharedPtr	m_session

const std::weak_ptr< EquationSystem >	m_equ

Detailed Description

Definition at line 44 of file FilterElectrogram.h.

Constructor & Destructor Documentation

◆ FilterElectrogram()

Nektar::FilterElectrogram::FilterElectrogram	(	const LibUtilities::SessionReaderSharedPtr &	pSession,
		const std::shared_ptr< SolverUtils::EquationSystem > &	pEquation,
		const ParamMap &	pParams
	)

Electrogram filter constructor.

Definition at line 50 of file FilterElectrogram.cpp.

    : Filter(pSession, pEquation)
{
    // OutputFile
    auto it = pParams.find("OutputFile");
    if (it == pParams.end())
    {
        m_outputFile = m_session->GetSessionName();
    }
    else
    {
        ASSERTL0(it->second.length() > 0, "Missing parameter 'OutputFile'.");
        m_outputFile = it->second;
    }
    if (!(m_outputFile.length() >= 4 &&
          m_outputFile.substr(m_outputFile.length() - 4) == ".ecg"))
    {
        m_outputFile += ".ecg";
    }
 
    // OutputFrequency
    it = pParams.find("OutputFrequency");
    if (it == pParams.end())
    {
        m_outputFrequency = 1;
    }
    else
    {
        LibUtilities::Equation equ(m_session->GetInterpreter(), it->second);
        m_outputFrequency = floor(equ.Evaluate());
    }
 
    // Points
    it = pParams.find("Points");
    ASSERTL0(it != pParams.end(), "Missing parameter 'Points'.");
    m_electrogramStream.str(it->second);
    m_index = 0;
}

References ASSERTL0, Nektar::LibUtilities::Equation::Evaluate(), m_electrogramStream, m_index, m_outputFile, m_outputFrequency, and Nektar::SolverUtils::Filter::m_session.

◆ ~FilterElectrogram()

Nektar::FilterElectrogram::~FilterElectrogram ( )

override

Electrogram filter destructor.

Definition at line 95 of file FilterElectrogram.cpp.

96{

97}

Member Function Documentation

◆ create()

static SolverUtils::FilterSharedPtr Nektar::FilterElectrogram::create	(	const LibUtilities::SessionReaderSharedPtr &	pSession,
		const std::shared_ptr< SolverUtils::EquationSystem > &	pEquation,
		const ParamMap &	pParams
	)

inlinestatic

Creates an instance of this class.

Definition at line 50 of file FilterElectrogram.h.

    {
        SolverUtils::FilterSharedPtr p =
            MemoryManager<FilterElectrogram>::AllocateSharedPtr(
                pSession, pEquation, pParams);
        return p;
    }

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), and CellMLToNektar.cellml_metadata::p.

◆ v_Finalise()

void Nektar::FilterElectrogram::v_Finalise	(	const Array< OneD, const MultiRegions::ExpListSharedPtr > &	pFields,
		const NekDouble &	time
	)

overrideprotectedvirtual

Finalise the electrogram filter and close output file.

Implements Nektar::SolverUtils::Filter.

Definition at line 259 of file FilterElectrogram.cpp.

{
    if (pFields[0]->GetComm()->GetRank() == 0)
    {
        m_outputStream.close();
    }
}

References m_outputStream.

◆ v_Initialise()

void Nektar::FilterElectrogram::v_Initialise	(	const Array< OneD, const MultiRegions::ExpListSharedPtr > &	pFields,
		const NekDouble &	time
	)

overrideprotectedvirtual

Initialises the electrogram filter and open output file.

Implements Nektar::SolverUtils::Filter.

Definition at line 102 of file FilterElectrogram.cpp.

{
    ASSERTL0(!m_electrogramStream.fail(), "No history points in stream.");
 
    m_index = 0;
    Array<OneD, NekDouble> gloCoord(3, 0.0);
    LibUtilities::CommSharedPtr vComm = pFields[0]->GetComm();
 
    // Read electrogram points
    // Always use dim = 3 to allow electrode to be above surface
    const size_t dim = 3;
    size_t i         = 0;
 
    while (!m_electrogramStream.fail())
    {
        m_electrogramStream >> gloCoord[0] >> gloCoord[1] >> gloCoord[2];
        if (!m_electrogramStream.fail())
        {
            SpatialDomains::PointGeomSharedPtr vert =
                MemoryManager<SpatialDomains::PointGeom>::AllocateSharedPtr(
                    dim, i, gloCoord[0], gloCoord[1], gloCoord[2]);
 
            m_electrogramPoints.push_back(vert);
            ++i;
        }
    }
 
    if (vComm->GetRank() == 0)
    {
        // Open output stream
        m_outputStream.open(m_outputFile.c_str());
        m_outputStream << "# Electrogram data for variables (:";
 
        for (size_t i = 0; i < pFields.size(); ++i)
        {
            m_outputStream << m_session->GetVariable(i) << ",";
        }
 
        m_outputStream << ") at points:" << endl;
 
        for (size_t i = 0; i < m_electrogramPoints.size(); ++i)
        {
            m_electrogramPoints[i]->GetCoords(gloCoord[0], gloCoord[1],
                                              gloCoord[2]);
 
            m_outputStream << "# \t" << i;
            m_outputStream.width(8);
            m_outputStream << gloCoord[0];
            m_outputStream.width(8);
            m_outputStream << gloCoord[1];
            m_outputStream.width(8);
            m_outputStream << gloCoord[2];
            m_outputStream << endl;
        }
    }
 
    // Compute the distance function for each electrogram point
    const size_t nq   = pFields[0]->GetNpoints();
    const size_t npts = m_electrogramPoints.size();
    NekDouble px, py, pz;
    m_grad_R_x = Array<OneD, Array<OneD, NekDouble>>(npts);
    m_grad_R_y = Array<OneD, Array<OneD, NekDouble>>(npts);
    m_grad_R_z = Array<OneD, Array<OneD, NekDouble>>(npts);
 
    Array<OneD, NekDouble> oneOverR(nq, 0.0);
 
    for (size_t i = 0; i < npts; ++i)
    {
        m_grad_R_x[i] = Array<OneD, NekDouble>(nq, 0.0);
        m_grad_R_y[i] = Array<OneD, NekDouble>(nq, 0.0);
        m_grad_R_z[i] = Array<OneD, NekDouble>(nq, 0.0);
 
        Array<OneD, NekDouble> x(nq, 0.0);
        Array<OneD, NekDouble> y(nq, 0.0);
        Array<OneD, NekDouble> z(nq, 0.0);
 
        // Compute 1/R
        m_electrogramPoints[i]->GetCoords(px, py, pz);
        pFields[0]->GetCoords(x, y, z);
 
        Vmath::Sadd(nq, -px, x, 1, x, 1);
        Vmath::Sadd(nq, -py, y, 1, y, 1);
        Vmath::Sadd(nq, -pz, z, 1, z, 1);
        Vmath::Vvtvvtp(nq, x, 1, x, 1, y, 1, y, 1, oneOverR, 1);
        Vmath::Vvtvp(nq, z, 1, z, 1, oneOverR, 1, oneOverR, 1);
        Vmath::Vsqrt(nq, oneOverR, 1, oneOverR, 1);
        Vmath::Sdiv(nq, 1.0, oneOverR, 1, oneOverR, 1);
 
        // Compute grad 1/R
        pFields[0]->PhysDeriv(oneOverR, m_grad_R_x[i], m_grad_R_y[i],
                              m_grad_R_z[i]);
    }
 
    // Compute electrogram point for initial condition
    v_Update(pFields, time);
}

References Nektar::MemoryManager< DataType >::AllocateSharedPtr(), ASSERTL0, m_electrogramPoints, m_electrogramStream, m_grad_R_x, m_grad_R_y, m_grad_R_z, m_index, m_outputFile, m_outputStream, Nektar::SolverUtils::Filter::m_session, Vmath::Sadd(), Vmath::Sdiv(), v_Update(), Vmath::Vsqrt(), Vmath::Vvtvp(), Vmath::Vvtvvtp(), and Nektar::UnitTests::z().

◆ v_IsTimeDependent()

bool Nektar::FilterElectrogram::v_IsTimeDependent ( )

overrideprotectedvirtual

Filter is time-dependent and should be called at each time-step.

Implements Nektar::SolverUtils::Filter.

Definition at line 272 of file FilterElectrogram.cpp.

{
    return true;
}

◆ v_Update()

void Nektar::FilterElectrogram::v_Update	(	const Array< OneD, const MultiRegions::ExpListSharedPtr > &	pFields,
		const NekDouble &	time
	)

overrideprotectedvirtual

Compute extracellular potential at egm points at current time.

Implements Nektar::SolverUtils::Filter.

Definition at line 204 of file FilterElectrogram.cpp.

{
    // Only output every m_outputFrequency.
    if ((m_index++) % m_outputFrequency)
    {
        return;
    }
 
    const size_t nq                   = pFields[0]->GetNpoints();
    const size_t npoints              = m_electrogramPoints.size();
    LibUtilities::CommSharedPtr vComm = pFields[0]->GetComm();
 
    size_t i = 0;
    Array<OneD, NekDouble> e(npoints);
 
    // Compute grad V
    Array<OneD, NekDouble> grad_V_x(nq), grad_V_y(nq), grad_V_z(nq);
    pFields[0]->PhysDeriv(pFields[0]->GetPhys(), grad_V_x, grad_V_y, grad_V_z);
 
    for (i = 0; i < npoints; ++i)
    {
        // Multiply together
        Array<OneD, NekDouble> output(nq);
        Vmath::Vvtvvtp(nq, m_grad_R_x[i], 1, grad_V_x, 1, m_grad_R_y[i], 1,
                       grad_V_y, 1, output, 1);
        Vmath::Vvtvp(nq, m_grad_R_z[i], 1, grad_V_z, 1, output, 1, output, 1);
 
        e[i] = pFields[0]->Integral(output);
    }
 
    // Exchange history data
    // This could be improved to reduce communication but works for now
    vComm->AllReduce(e, LibUtilities::ReduceSum);
 
    // Only the root process writes out electrogram data
    if (vComm->GetRank() == 0)
    {
        m_outputStream.width(8);
        m_outputStream << setprecision(6) << time;
 
        // Write data values point by point
        for (i = 0; i < m_electrogramPoints.size(); ++i)
        {
            m_outputStream.width(25);
            m_outputStream << setprecision(16) << e[i];
        }
        m_outputStream << endl;
    }
}

References m_electrogramPoints, m_grad_R_x, m_grad_R_y, m_grad_R_z, m_index, m_outputFrequency, m_outputStream, Nektar::LibUtilities::ReduceSum, Vmath::Vvtvp(), and Vmath::Vvtvvtp().

Referenced by v_Initialise().

Friends And Related Function Documentation

◆ MemoryManager< FilterElectrogram >

friend class MemoryManager< FilterElectrogram >

friend

Definition at line 1 of file FilterElectrogram.h.

Member Data Documentation

◆ className

std::string Nektar::FilterElectrogram::className

static

Initial value:

=
    SolverUtils::GetFilterFactory().RegisterCreatorFunction(
        "Electrogram", FilterElectrogram::create)

Name of the class.

Definition at line 62 of file FilterElectrogram.h.

◆ m_electrogramPoints

SpatialDomains::PointGeomVector Nektar::FilterElectrogram::m_electrogramPoints

private

List of electrogram points.

Definition at line 97 of file FilterElectrogram.h.

Referenced by v_Initialise(), and v_Update().

◆ m_electrogramStream

std::stringstream Nektar::FilterElectrogram::m_electrogramStream

private

Point coordinate input string.

Definition at line 107 of file FilterElectrogram.h.

Referenced by FilterElectrogram(), and v_Initialise().

◆ m_grad_R_x

Array<OneD, Array<OneD, NekDouble> > Nektar::FilterElectrogram::m_grad_R_x

private

Gradient of the radius from each electrogram point in x-direction.

Definition at line 91 of file FilterElectrogram.h.

Referenced by v_Initialise(), and v_Update().

◆ m_grad_R_y

Array<OneD, Array<OneD, NekDouble> > Nektar::FilterElectrogram::m_grad_R_y

private

Gradient of the radius from each electrogram point in y-direction.

Definition at line 93 of file FilterElectrogram.h.

Referenced by v_Initialise(), and v_Update().

◆ m_grad_R_z

Array<OneD, Array<OneD, NekDouble> > Nektar::FilterElectrogram::m_grad_R_z

private

Gradient of the radius from each electrogram point in z-direction.

Definition at line 95 of file FilterElectrogram.h.

Referenced by v_Initialise(), and v_Update().

◆ m_index

unsigned int Nektar::FilterElectrogram::m_index

private

Counts number of calls to update (number of timesteps)

Definition at line 99 of file FilterElectrogram.h.

Referenced by FilterElectrogram(), v_Initialise(), and v_Update().

◆ m_outputFile

std::string Nektar::FilterElectrogram::m_outputFile

private

Filename to output electrogram data to.

Definition at line 103 of file FilterElectrogram.h.

Referenced by FilterElectrogram(), and v_Initialise().

◆ m_outputFrequency

unsigned int Nektar::FilterElectrogram::m_outputFrequency

private

Number of timesteps between outputs.

Definition at line 101 of file FilterElectrogram.h.

Referenced by FilterElectrogram(), and v_Update().

◆ m_outputStream

std::ofstream Nektar::FilterElectrogram::m_outputStream

private

Output file stream for electrogram data.

Definition at line 105 of file FilterElectrogram.h.

Referenced by v_Finalise(), v_Initialise(), and v_Update().

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FilterElectrogram()

◆ ~FilterElectrogram()

Member Function Documentation

◆ create()

◆ v_Finalise()

◆ v_Initialise()

◆ v_IsTimeDependent()

◆ v_Update()

Friends And Related Function Documentation

◆ MemoryManager< FilterElectrogram >

Member Data Documentation

◆ className

◆ m_electrogramPoints

◆ m_electrogramStream

◆ m_grad_R_x

◆ m_grad_R_y

◆ m_grad_R_z

◆ m_index

◆ m_outputFile

◆ m_outputFrequency

◆ m_outputStream