FilterHilbertFFTPhase.cpp

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///////////////////////////////////////////////////////////////////////////////
//
// File FilterHilbertFFTPhase.cpp
//
// 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
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
// DEALINGS IN THE SOFTWARE.
//
// Description: Outputs phase fields during time-stepping.
//
///////////////////////////////////////////////////////////////////////////////
 
#include <CardiacEPSolver/Filters/FilterHilbertFFTPhase.h>
 
namespace Nektar
{
std::string FilterHilbertFFTPhase::className =
    SolverUtils::GetFilterFactory().RegisterCreatorFunction(
        "HilbertPhase", FilterHilbertFFTPhase::create);
 
FilterHilbertFFTPhase::FilterHilbertFFTPhase(
    const LibUtilities::SessionReaderSharedPtr &pSession,
    const std::shared_ptr<SolverUtils::EquationSystem> &pEquation,
    const ParamMap &pParams)
    : Filter(pSession, pEquation)
{
    std::string ext = "";
    m_outputFile    = Filter::SetupOutput(ext, pParams);
 
    ASSERTL0(pParams.find("OutputFrequency") != pParams.end(),
             "Missing parameter 'OutputFrequency'."); // Sampling frequency =
                                                      // per number of timesteps
    LibUtilities::Equation equ(m_session->GetInterpreter(),
                               pParams.find("OutputFrequency")->second);
    m_outputFrequency = floor(equ.Evaluate());
 
    ASSERTL0(pParams.find("WindowSize") != pParams.end(),
             "Missing parameter 'WindowSize'.");
    LibUtilities::Equation equ1(m_session->GetInterpreter(),
                                pParams.find("WindowSize")->second);
    m_window = floor(equ1.Evaluate()); // No. of output steps taken in each FFT
    ASSERTL0(m_window % 2 == 0, "'WindowSize' must be even.");
 
    ASSERTL0(pParams.find("OverlapSize") != pParams.end(),
             "Missing parameter 'OverlapSize'.");
    LibUtilities::Equation equ2(m_session->GetInterpreter(),
                                pParams.find("OverlapSize")->second);
    m_overlap = floor(equ2.Evaluate());
    ASSERTL0(m_window > m_overlap,
             "'OverlapSize' must be smaller than 'WindowSize'.");
 
    if (pParams.find("MeanV") != pParams.end())
    {
        provided_mean = true;
        LibUtilities::Equation equ3(m_session->GetInterpreter(),
                                    pParams.find("MeanV")->second);
        m_mean = equ3.Evaluate();
    }
 
    if (pParams.find("LinearTransitionOverlap") != pParams.end())
    {
        linear_trans =
            (pParams.find("LinearTransitionOverlap")->second == "true");
    }
 
    m_outputIndex = 0;
    m_index       = 0;
 
    m_fld = LibUtilities::FieldIO::CreateDefault(pSession);
}
 
FilterHilbertFFTPhase::~FilterHilbertFFTPhase()
{
}
 
void FilterHilbertFFTPhase::v_Initialise(
    const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields,
    [[maybe_unused]] const NekDouble &time)
{
    m_index       = 0;
    m_outputIndex = 0;
    vCounter      = 0;
 
    m_TimeStep = pFields[0]->GetSession()->GetParameter("TimeStep");
 
    npoints        = pFields[0]->GetPhys().size();
    oldV           = Array<OneD, NekDouble>(npoints * m_window);
    oldV_zero_mean = Array<OneD, NekDouble>(npoints * m_window);
    fcoef          = Array<OneD, NekDouble>(npoints * m_window);
    h              = Array<OneD, NekDouble>(npoints * m_window);
    overlap_phase  = Array<OneD, NekDouble>(npoints * m_overlap);
    std::fill_n(&overlap_phase[0], npoints * m_overlap, 0.0);
 
    // Initialise FFTW
    fftw_r2r_kind *fwd_kind = new fftw_r2r_kind[npoints];
    std::fill_n(fwd_kind, npoints, FFTW_R2HC);
    plan_forward = fftw_plan_many_r2r(
        1, &m_window, npoints, &oldV_zero_mean[0], &m_window, npoints, 1,
        &fcoef[0], &m_window, npoints, 1, &fwd_kind[0], FFTW_ESTIMATE);
 
    fftw_r2r_kind *bwd_kind = new fftw_r2r_kind[npoints];
    std::fill_n(bwd_kind, npoints, FFTW_HC2R);
    plan_backward = fftw_plan_many_r2r(1, &m_window, npoints, &fcoef[0],
                                       &m_window, npoints, 1, &h[0], &m_window,
                                       npoints, 1, &bwd_kind[0], FFTW_ESTIMATE);
 
    delete[] fwd_kind;
    delete[] bwd_kind;
    v_Update(pFields, 0.0);
}
 
void FilterHilbertFFTPhase::v_Update(
    const Array<OneD, const MultiRegions::ExpListSharedPtr> &pFields,
    [[maybe_unused]] const NekDouble &time)
{
    if (m_index++ % m_outputFrequency > 0)
    {
        return;
    }
 
    // Store old data
    Array<OneD, NekDouble> currentV = pFields[0]->GetPhys();
    memcpy(&oldV[vCounter * npoints], &currentV[0],
           npoints * sizeof(NekDouble));
    vCounter++;
 
    // Do Hilbert Transform and output phase
    if (vCounter == m_window)
    {
        // Zero mean
        if (!provided_mean)
        {
            for (int j = 0; j < npoints; ++j)
            {
                m_mean = 0.0;
                for (int i = 0; i < m_window; ++i)
                {
                    m_mean += oldV[i * npoints + j];
                }
                m_mean = m_mean / (double)m_window; // time-average
 
                for (int i = 0; i < m_window; ++i)
                {
                    oldV_zero_mean[i * npoints + j] =
                        oldV[i * npoints + j] - m_mean;
                }
            }
        }
        else // minus mean directly
        {
            for (int i = 0; i < npoints * m_window; ++i)
            {
                oldV_zero_mean[i] = oldV[i] - m_mean;
            }
        }
 
        // Do Hilbert Transform:
        fftw_execute(plan_forward);
        // Rearrange out: imag->real, -real->imag
        double tmp_fcoef;
        for (int i = 1; i < m_window / 2; ++i)
        {
            for (int j = 0; j < npoints; ++j)
            {
                tmp_fcoef = -fcoef[i * npoints + j] / m_window;
                fcoef[i * npoints + j] =
                    fcoef[(m_window - i) * npoints + j] / m_window;
                fcoef[(m_window - i) * npoints + j] = tmp_fcoef;
            }
        }
        std::fill_n(&fcoef[0], npoints, 0.0);
        std::fill_n(&fcoef[(m_window / 2) * npoints], npoints, 0.0);
        fftw_execute(plan_backward);
 
        // Output batch
        Array<OneD, NekDouble> phase_coeff(pFields[0]->GetNcoeffs());
        Array<OneD, NekDouble> phase(npoints);
 
        for (int t = 0; t < m_window - m_overlap; ++t)
        {
            std::stringstream vTmpFilename;
            std::string vOutputFilename;
            std::string ext = ".chk";
 
            vTmpFilename
                << fs::path(m_outputFile).replace_extension("").string() << "_"
                << m_outputIndex << ext;
            vOutputFilename = Filter::SetupOutput(ext, vTmpFilename.str());
 
            // Get FieldDefinitions and allocate Fielddata
            std::vector<LibUtilities::FieldDefinitionsSharedPtr> FieldDef =
                pFields[0]->GetFieldDefinitions();
            std::vector<std::vector<NekDouble>> FieldData(FieldDef.size());
 
            // Calculate phase
            if (t < m_overlap)
            {
                if (linear_trans)
                {
                    for (int i = 0; i < npoints; ++i)
                    {
                        phase[i] = ((double)(m_overlap - t) / m_overlap) *
                                       overlap_phase[t * npoints + i] +
                                   ((double)t / m_overlap) *
                                       atan2(h[t * npoints + i],
                                             oldV_zero_mean[t * npoints + i]);
                    }
                }
                else // simple average
                {
                    for (int i = 0; i < npoints; ++i)
                    {
                        phase[i] = 0.5 * overlap_phase[t * npoints + i] +
                                   0.5 * atan2(h[t * npoints + i],
                                               oldV_zero_mean[t * npoints + i]);
                    }
                }
            }
            else
            {
                for (int i = 0; i < npoints; ++i)
                {
                    phase[i] = atan2(h[t * npoints + i],
                                     oldV_zero_mean[t * npoints + i]);
                }
            }
 
            // Convert to coefficient space
            pFields[0]->FwdTransLocalElmt(phase, phase_coeff);
 
            // for each item in FieldDef
            //      push "phase" to FieldDef[i]->m_fields
            //      call AppendFieldData(FieldDef[i], FieldData[i], data)
            for (int i = 0; i < FieldDef.size(); ++i)
            {
                FieldDef[i]->m_fields.push_back("phase");
                pFields[0]->AppendFieldData(FieldDef[i], FieldData[i],
                                            phase_coeff);
            }
 
            // Update time in field info if required
            LibUtilities::FieldMetaDataMap fieldMetaDataMap;
            fieldMetaDataMap["Time"] = boost::lexical_cast<std::string>(
                m_outputIndex * m_outputFrequency * m_TimeStep);
 
            m_fld->Write(vOutputFilename, FieldDef, FieldData,
                         fieldMetaDataMap);
            m_outputIndex++;
        }
 
        // Save phase for next iter
        for (int t = m_window - m_overlap; t < m_window; ++t)
        {
            for (int i = 0; i < npoints; ++i)
            {
                overlap_phase[(t - m_window + m_overlap) * npoints + i] =
                    atan2(h[t * npoints + i], oldV_zero_mean[t * npoints + i]);
            }
        }
 
        // Move overlap part to front
        memcpy(&oldV[0], &oldV[(m_window - m_overlap) * npoints],
               npoints * m_overlap * sizeof(NekDouble));
        vCounter = m_overlap;
    }
}
 
void FilterHilbertFFTPhase::v_Finalise(
    [[maybe_unused]] const Array<OneD, const MultiRegions::ExpListSharedPtr>
        &pFields,
    [[maybe_unused]] const NekDouble &time)
{
}
 
bool FilterHilbertFFTPhase::v_IsTimeDependent()
{
    return true;
}
} // namespace Nektar