#include <FilterElectrogram.h>

Inheritance diagram for Nektar::FilterElectrogram:

Collaboration diagram for Nektar::FilterElectrogram:

Public Member Functions
	FilterElectrogram (const LibUtilities::SessionReaderSharedPtr &pSession, const ParamMap &pParams)
	Electrogram filter constructor. More...

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

Public Member Functions inherited from Nektar::SolverUtils::Filter
SOLVER_UTILS_EXPORT	Filter (const LibUtilities::SessionReaderSharedPtr &pSession)

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 ParamMap &pParams)
	Creates an instance of this class. More...

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

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

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

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

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

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

Detailed Description

Definition at line 45 of file FilterElectrogram.h.

Constructor & Destructor Documentation

Nektar::FilterElectrogram::FilterElectrogram	(	const LibUtilities::SessionReaderSharedPtr &	pSession,
		const ParamMap &	pParams
	)

Electrogram filter constructor.

Definition at line 52 of file FilterElectrogram.cpp.

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

     : Filter(pSession)
 {
     ParamMap::const_iterator it;
 
     // OutputFile
     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, 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;
 }

Nektar::FilterElectrogram::~FilterElectrogram ( )

virtual

Electrogram filter destructor.

Definition at line 99 of file FilterElectrogram.cpp.

 {
 
 }

Member Function Documentation

static SolverUtils::FilterSharedPtr Nektar::FilterElectrogram::create	(	const LibUtilities::SessionReaderSharedPtr &	pSession,
		const ParamMap &	pParams
	)

inlinestatic

Creates an instance of this class.

Definition at line 51 of file FilterElectrogram.h.

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

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

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

protectedvirtual

Finalise the electrogram filter and close output file.

Implements Nektar::SolverUtils::Filter.

Definition at line 272 of file FilterElectrogram.cpp.

References m_outputStream.

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

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

protectedvirtual

Initialises the electrogram filter and open output file.

Implements Nektar::SolverUtils::Filter.

Definition at line 108 of file FilterElectrogram.cpp.

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, npts, Vmath::Sadd(), Vmath::Sdiv(), v_Update(), Vmath::Vsqrt(), Vmath::Vvtvp(), and Vmath::Vvtvvtp().

 {
     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 int dim = 3;
     int 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 (i = 0; i < pFields.num_elements(); ++i)
         {
             m_outputStream << m_session->GetVariable(i) <<",";
         }
 
         m_outputStream << ") at points:" << endl;
 
         for (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 unsigned int nq   = pFields[0]->GetNpoints();
     const unsigned int 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> x(nq);
     Array<OneD, NekDouble> y(nq);
     Array<OneD, NekDouble> z(nq);
 
     Array<OneD, NekDouble> oneOverR(nq);
     for (unsigned int i = 0; i < npts; ++i)
     {
         m_grad_R_x[i] = Array<OneD, NekDouble>(nq);
         m_grad_R_y[i] = Array<OneD, NekDouble>(nq);
         m_grad_R_z[i] = Array<OneD, NekDouble>(nq);
 
         // 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);
 }

bool Nektar::FilterElectrogram::v_IsTimeDependent ( )

protectedvirtual

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

Implements Nektar::SolverUtils::Filter.

Definition at line 286 of file FilterElectrogram.cpp.

 {
     return true;
 }

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

protectedvirtual

Compute extracellular potential at egm points at current time.

Implements Nektar::SolverUtils::Filter.

Definition at line 214 of file FilterElectrogram.cpp.

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().

 {
     // Only output every m_outputFrequency.
     if ((m_index++) % m_outputFrequency)
     {
         return;
     }
 
     const unsigned int nq = pFields[0]->GetNpoints();
     const unsigned int npoints = m_electrogramPoints.size();
     LibUtilities::CommSharedPtr vComm = pFields[0]->GetComm();
 
     unsigned int 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;
     }
 }

Friends And Related Function Documentation

friend class MemoryManager< FilterElectrogram >

friend

Definition at line 48 of file FilterElectrogram.h.

Member Data Documentation

std::string Nektar::FilterElectrogram::className

static

Initial value:

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

Name of the class.

Definition at line 60 of file FilterElectrogram.h.

SpatialDomains::PointGeomVector Nektar::FilterElectrogram::m_electrogramPoints

private

List of electrogram points.

Definition at line 94 of file FilterElectrogram.h.

Referenced by v_Initialise(), and v_Update().

std::stringstream Nektar::FilterElectrogram::m_electrogramStream

private

Point coordinate input string.

Definition at line 104 of file FilterElectrogram.h.

Referenced by FilterElectrogram(), and v_Initialise().

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 88 of file FilterElectrogram.h.

Referenced by v_Initialise(), and v_Update().

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 90 of file FilterElectrogram.h.

Referenced by v_Initialise(), and v_Update().

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 92 of file FilterElectrogram.h.

Referenced by v_Initialise(), and v_Update().

unsigned int Nektar::FilterElectrogram::m_index

private

Counts number of calls to update (number of timesteps)

Definition at line 96 of file FilterElectrogram.h.

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

std::string Nektar::FilterElectrogram::m_outputFile

private

Filename to output electrogram data to.

Definition at line 100 of file FilterElectrogram.h.

Referenced by FilterElectrogram(), and v_Initialise().

unsigned int Nektar::FilterElectrogram::m_outputFrequency

private

Number of timesteps between outputs.

Definition at line 98 of file FilterElectrogram.h.

Referenced by FilterElectrogram(), and v_Update().

std::ofstream Nektar::FilterElectrogram::m_outputStream

private

Output file stream for electrogram data.

Definition at line 102 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

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation