ActivationOutputModifier.cpp

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*/
 
#include "ActivationOutputModifier.hpp"
#include "OutputFileHandler.hpp"
#include "HeartConfig.hpp"
 
void ActivationOutputModifier::InitialiseAtStart(DistributedVectorFactory* pVectorFactory, const std::vector<unsigned>& rNodePermutation)
{
    mLocalSize = pVectorFactory->GetLocalOwnership();
    mFirstActivitationTimes.resize(mLocalSize, -1.0);
    mFirstRecoveryTimes.resize(mLocalSize, -1.0);
    mSecondActivitationTimes.resize(mLocalSize, -1.0);
    mSecondRecoveryTimes.resize(mLocalSize, -1.0);
}
 
void ActivationOutputModifier::FinaliseAtEnd()
{
    //Dump out all data in a round-robin fashion
    OutputFileHandler output_handler(HeartConfig::Instance()->GetOutputDirectory(), false);
 
    // Belt and braces
    std::stringstream filepath_process_specific;
    filepath_process_specific << mFilename << "." << PetscTools::GetMyRank();
    out_stream file_stream_process_specific = output_handler.OpenOutputFile(filepath_process_specific.str().c_str());
    for (unsigned i=0; i<mLocalSize; i++)
    {
        (*file_stream_process_specific) << mFirstActivitationTimes[i] <<",\t"
                << mFirstRecoveryTimes[i] <<",\t"
                << mSecondActivitationTimes[i] <<",\t"
                << mSecondRecoveryTimes[i] <<"\n";
    }
    file_stream_process_specific->close();
 
    PetscTools::BeginRoundRobin();
    {
        out_stream file_stream = out_stream(NULL);
        // Open the file as new or append
        if (PetscTools::AmMaster())
        {
            file_stream = output_handler.OpenOutputFile(mFilename);
        }
        else
        {
            file_stream = output_handler.OpenOutputFile(mFilename, std::ios::app);
        }
        for (unsigned i=0; i<mLocalSize; i++)
        {
            (*file_stream) << mFirstActivitationTimes[i] <<",\t"
                    << mFirstRecoveryTimes[i] <<",\t"
                    << mSecondActivitationTimes[i] <<",\t"
                    << mSecondRecoveryTimes[i] <<"\n";
        }
        file_stream->close();
    }
    PetscTools::EndRoundRobin();
}
 
void ActivationOutputModifier::ProcessSolutionAtTimeStep(double time, Vec solution, unsigned problemDim)
{
    double* p_solution;
    VecGetArray(solution, &p_solution);
    for (unsigned local_index=0; local_index < mLocalSize; local_index++)
    {
        double v = p_solution[local_index*problemDim];
        if (v > mThreshold && mFirstActivitationTimes[local_index] < 0.0)
        {
            mFirstActivitationTimes[local_index] = time;
        }
// LCOV_EXCL_START // Continuous tests are not long enough to allow recover
        else if (mFirstActivitationTimes[local_index] >= 0.0 && mFirstRecoveryTimes[local_index] < 0.0 && v < mThreshold)
        {
            mFirstRecoveryTimes[local_index] = time;
        }
        else if (mFirstRecoveryTimes[local_index] >= 0.0 && mSecondActivitationTimes[local_index] < 0.0 && v > mThreshold)
        {
            mSecondActivitationTimes[local_index] = time;
        }
        else if (mSecondActivitationTimes[local_index] >= 0.0 && mSecondRecoveryTimes[local_index] < 0.0 && v < mThreshold)
        {
            mSecondRecoveryTimes[local_index] = time;
        }
// LCOV_EXCL_STOP // Continuous tests are not long enough to allow recover
    }
    VecRestoreArray(solution, &p_solution);
}
 
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(ActivationOutputModifier)