FilterElectrogram.h

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///////////////////////////////////////////////////////////////////////////////
//
// File FilterElectrogram.h
//
// For more information, please see: http://www.nektar.info
//
// The MIT License
//
// Copyright (c) 2006 Division of Applied Mathematics, Brown University (USA),
// Department of Aeronautics, Imperial College London (UK), and Scientific
// Computing and Imaging Institute, University of Utah (USA).
//
// License for the specific language governing rights and limitations under
// Permission is hereby granted, free of charge, to any person obtaining a
// copy of this software and associated documentation files (the "Software"),
// to deal in the Software without restriction, including without limitation
// the rights to use, copy, modify, merge, publish, distribute, sublicense,
// and/or sell copies of the Software, and to permit persons to whom the
// Software is furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included
// in all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
// THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: Outputs virtual electrograms at specific locations.
//
///////////////////////////////////////////////////////////////////////////////

#ifndef NEKTAR_SOLVERUTILS_FILTERS_FILTERELECTROGRAM_H
#define NEKTAR_SOLVERUTILS_FILTERS_FILTERELECTROGRAM_H

#include <CardiacEPSolver/CellModels/CellModel.h>
#include <SolverUtils/Filters/Filter.h>

namespace Nektar
{
    class FilterElectrogram : public SolverUtils::Filter
    {
    public:
        friend class MemoryManager<FilterElectrogram>;

        /// Creates an instance of this class
        static SolverUtils::FilterSharedPtr create(
            const LibUtilities::SessionReaderSharedPtr &pSession,
            const std::map<std::string, std::string>   &pParams) {
            SolverUtils::FilterSharedPtr p = 
                MemoryManager<FilterElectrogram>::AllocateSharedPtr(
                        pSession, pParams);
            return p;
        }

        /// Name of the class
        static std::string className;

        /// Electrogram filter constructor
        FilterElectrogram(
            const LibUtilities::SessionReaderSharedPtr &pSession,
            const std::map<std::string, std::string>   &pParams);

        /// Electrogram filter destructor
        virtual ~FilterElectrogram();

    protected:
        /// Initialises the electrogram filter and open output file.
        virtual void v_Initialise(
            const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields,
            const NekDouble &time);
        /// Compute extracellular potential at egm points at current time.
        virtual void v_Update(
            const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields, 
            const NekDouble &time);
        /// Finalise the electrogram filter and close output file.
        virtual void v_Finalise(
            const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields, 
            const NekDouble &time);
        /// Filter is time-dependent and should be called at each time-step.
        virtual bool v_IsTimeDependent();

    private:
        /// Gradient of the radius from each electrogram point in x-direction
        Array<OneD, Array<OneD, NekDouble> >    m_grad_R_x;
        /// Gradient of the radius from each electrogram point in y-direction
        Array<OneD, Array<OneD, NekDouble> >    m_grad_R_y;
        /// Gradient of the radius from each electrogram point in z-direction
        Array<OneD, Array<OneD, NekDouble> >    m_grad_R_z;
        /// List of electrogram points
        SpatialDomains::PointGeomVector         m_electrogramPoints;
        /// Counts number of calls to update (number of timesteps)
        unsigned int                            m_index;
        /// Number of timesteps between outputs
        unsigned int                            m_outputFrequency;
        /// Filename to output electrogram data to
        std::string                             m_outputFile;
        /// Output file stream for electrogram data
        std::ofstream                           m_outputStream;
        /// Point coordinate input string
        std::stringstream                       m_electrogramStream;
    };
}

#endif