PostProcessingWriter.cpp

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#include "UblasCustomFunctions.hpp"
#include "HeartConfig.hpp"
#include "PostProcessingWriter.hpp"
#include "PetscTools.hpp"
#include "OutputFileHandler.hpp"
#include "DistanceMapCalculator.hpp"
#include "PseudoEcgCalculator.hpp"
#include "Version.hpp"
#include "HeartEventHandler.hpp"

#include <iostream>

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::PostProcessingWriter(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& rMesh,
                                                                   std::string directory,
                                                                   std::string hdf5File,
                                                                   bool makeAbsolute,
                                                                   std::string voltageName)
        : mDirectory(directory),
          mHdf5File(hdf5File),
          mMakeAbsolute(makeAbsolute),
          mVoltageName(voltageName),
          mrMesh(rMesh)
{
    mLo = mrMesh.GetDistributedVectorFactory()->GetLow();
    mHi = mrMesh.GetDistributedVectorFactory()->GetHigh();
    mpDataReader = new Hdf5DataReader(directory, hdf5File, makeAbsolute);
    mpCalculator = new PropagationPropertiesCalculator(mpDataReader,voltageName);
    //check that the hdf file was generated by simulations from the same mesh
    assert(mpDataReader->GetNumberOfRows() == mrMesh.GetNumNodes());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WritePostProcessingFiles()
{
    //Check that post-processing is really needed
    assert(HeartConfig::Instance()->IsPostProcessingRequested());
    //Check that it's safe to send the results to the (hard-coded) subfolder for Meshalyzer/CMGui
    assert(HeartConfig::Instance()->GetVisualizeWithMeshalyzer() || HeartConfig::Instance()->GetVisualizeWithCmgui());

    // Please note that only the master processor should write to file.
    // Each of the private methods called here takes care of checking.

    if (HeartConfig::Instance()->IsApdMapsRequested())
    {
        std::vector<std::pair<double,double> > apd_maps;
        HeartConfig::Instance()->GetApdMaps(apd_maps);
        for (unsigned i=0; i<apd_maps.size(); i++)
        {
            WriteApdMapFile(apd_maps[i].first, apd_maps[i].second);
        }
    }

    if (HeartConfig::Instance()->IsUpstrokeTimeMapsRequested())
    {
        std::vector<double> upstroke_time_maps;
        HeartConfig::Instance()->GetUpstrokeTimeMaps(upstroke_time_maps);
        for (unsigned i=0; i<upstroke_time_maps.size(); i++)
        {
            WriteUpstrokeTimeMap(upstroke_time_maps[i]);
        }
    }

    if (HeartConfig::Instance()->IsMaxUpstrokeVelocityMapRequested())
    {
        std::vector<double> upstroke_velocity_maps;
        HeartConfig::Instance()->GetMaxUpstrokeVelocityMaps(upstroke_velocity_maps);
        for (unsigned i=0; i<upstroke_velocity_maps.size(); i++)
        {
            WriteMaxUpstrokeVelocityMap(upstroke_velocity_maps[i]);
        }
    }

    if (HeartConfig::Instance()->IsConductionVelocityMapsRequested())
    {
        std::vector<unsigned> conduction_velocity_maps;
        HeartConfig::Instance()->GetConductionVelocityMaps(conduction_velocity_maps);

        //get the mesh here
        DistanceMapCalculator<ELEMENT_DIM, SPACE_DIM> dist_map_calculator(mrMesh);

        for (unsigned i=0; i<conduction_velocity_maps.size(); i++)
        {
            std::vector<double> distance_map;
            std::vector<unsigned> origin_surface;
            origin_surface.push_back(conduction_velocity_maps[i]);
            dist_map_calculator.ComputeDistanceMap(origin_surface, distance_map);
            WriteConductionVelocityMap(conduction_velocity_maps[i], distance_map);
        }
    }

    if (HeartConfig::Instance()->IsAnyNodalTimeTraceRequested())
    {
        std::vector<unsigned> requested_nodes;
        HeartConfig::Instance()->GetNodalTimeTraceRequested(requested_nodes);
        WriteVariablesOverTimeAtNodes(requested_nodes);
    }

    if (HeartConfig::Instance()->IsPseudoEcgCalculationRequested())
    {
        std::vector<ChastePoint<SPACE_DIM> > electrodes;
        HeartConfig::Instance()->GetPseudoEcgElectrodePositions(electrodes);

        for (unsigned i=0; i<electrodes.size(); i++)
        {
            PseudoEcgCalculator<ELEMENT_DIM,SPACE_DIM,1> calculator(mrMesh, electrodes[i], mDirectory, mHdf5File, mVoltageName, mMakeAbsolute);
            calculator.WritePseudoEcg();
        }
    }
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::~PostProcessingWriter()
{
    delete mpDataReader;
    delete mpCalculator;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WriteApdMapFile(double repolarisationPercentage, double threshold)
{
    std::vector<std::vector<double> > output_data = mpCalculator->CalculateAllActionPotentialDurationsForNodeRange(repolarisationPercentage, mLo, mHi, threshold);
    std::stringstream filename_stream;
    filename_stream << "Apd_" << repolarisationPercentage << "_" << threshold << "_Map.dat";
    WriteGenericFile(output_data, filename_stream.str());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WriteUpstrokeTimeMap(double threshold)
{
    std::vector<std::vector<double> > output_data;
    //Fill in data
    for (unsigned node_index = mLo; node_index < mHi; node_index++)
    {
        std::vector<double> upstroke_times;
        try
        {
            upstroke_times = mpCalculator->CalculateUpstrokeTimes(node_index, threshold);
            assert(upstroke_times.size() != 0);
        }
        catch(Exception& e)
        {
            upstroke_times.push_back(0);
            assert(upstroke_times.size() == 1);
        }
        output_data.push_back(upstroke_times);
    }
    std::stringstream filename_stream;
    filename_stream << "UpstrokeTimeMap_" << threshold << ".dat";
    WriteGenericFile(output_data, filename_stream.str());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WriteMaxUpstrokeVelocityMap(double threshold)
{
    std::vector<std::vector<double> > output_data;
    //Fill in data
    for (unsigned node_index = mLo; node_index < mHi; node_index++)
    {
        std::vector<double> upstroke_velocities;
        try
        {
            upstroke_velocities = mpCalculator->CalculateAllMaximumUpstrokeVelocities(node_index, threshold);
            assert(upstroke_velocities.size() != 0);
        }
        catch(Exception& e)
        {
            upstroke_velocities.push_back(0);
            assert(upstroke_velocities.size() ==1);
        }
        output_data.push_back(upstroke_velocities);
    }
    std::stringstream filename_stream;
    filename_stream << "MaxUpstrokeVelocityMap_" << threshold << ".dat";
    WriteGenericFile(output_data, filename_stream.str());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WriteConductionVelocityMap(unsigned originNode, std::vector<double> distancesFromOriginNode)
{
    //Fill in data
    std::vector<std::vector<double> > output_data;
    for (unsigned dest_node = mLo; dest_node < mHi; dest_node++)
    {
        std::vector<double> conduction_velocities;
        try
        {
            conduction_velocities = mpCalculator->CalculateAllConductionVelocities(originNode, dest_node, distancesFromOriginNode[dest_node]);
            assert(conduction_velocities.size() != 0);
        }
        catch(Exception& e)
        {
            conduction_velocities.push_back(0);
            assert(conduction_velocities.size() == 1);
        }
        output_data.push_back(conduction_velocities);
    }
    std::stringstream filename_stream;
    filename_stream << "ConductionVelocityFromNode" << originNode << ".dat";
    WriteGenericFile(output_data, filename_stream.str());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WriteAboveThresholdDepolarisationFile(double threshold )
{
    std::vector<std::vector<double> > output_data;

    //Fill in data
    for (unsigned node_index = mLo; node_index < mHi; node_index++)
    {
        std::vector<double> upstroke_velocities;
        std::vector<unsigned> above_threshold_depolarisations;
        std::vector<double> output_item;
        bool no_upstroke_occurred = false;

        try
        {
            upstroke_velocities = mpCalculator->CalculateAllMaximumUpstrokeVelocities(node_index, threshold);
            assert(upstroke_velocities.size() != 0);
        }
        catch(Exception& e)
        {
            upstroke_velocities.push_back(0);
            assert(upstroke_velocities.size() ==1);
            no_upstroke_occurred = true;
        }
        //this method won't throw any exception, so there is no need to put it into the try/catch
        above_threshold_depolarisations =  mpCalculator->CalculateAllAboveThresholdDepolarisations(node_index, threshold);

        //count the total above threshold depolarisations
        unsigned total_number_of_above_threshold_depolarisations = 0;
        for (unsigned ead_index = 0; ead_index< above_threshold_depolarisations.size();ead_index++)
        {
            total_number_of_above_threshold_depolarisations = total_number_of_above_threshold_depolarisations + above_threshold_depolarisations[ead_index];
        }

        //for this item, push back the number of upstrokes...
        if (no_upstroke_occurred)
        {
            output_item.push_back(0);
        }
        else
        {
            output_item.push_back(upstroke_velocities.size());
        }
        //... and the number of above threshold depolarisations
        output_item.push_back((double) total_number_of_above_threshold_depolarisations);

        output_data.push_back(output_item);
    }
    std::stringstream filename_stream;
    filename_stream << "AboveThresholdDepolarisations" << threshold << ".dat";
    WriteGenericFile(output_data, filename_stream.str());
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WriteVariablesOverTimeAtNodes(std::vector<unsigned>& rNodeIndices)
{
    std::vector<std::string> variable_names = mpDataReader->GetVariableNames();

    //we will write one file per variable in the hdf5 file
    for (unsigned name_index=0; name_index < variable_names.size(); name_index++)
    {
        std::vector<std::vector<double> > output_data;
        if (PetscTools::AmMaster())//only master process fills the data structure
        {
            //allocate memory: NXM matrix where N = number of time steps and M number of requested nodes
            output_data.resize( mpDataReader->GetUnlimitedDimensionValues().size() );
            for (unsigned j = 0; j < mpDataReader->GetUnlimitedDimensionValues().size(); j++)
            {
                output_data[j].resize(rNodeIndices.size());
            }

            for (unsigned requested_index = 0; requested_index < rNodeIndices.size(); requested_index++)
            {
                unsigned node_index = rNodeIndices[requested_index];

                //handle permutation, if any
                if ( (mrMesh.rGetNodePermutation().size() != 0) &&
                      !HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering() )
                {
                    node_index = mrMesh.rGetNodePermutation()[ rNodeIndices[requested_index] ];
                }

                //grab the data from the hdf5 file.
                std::vector<double> time_series =  mpDataReader->GetVariableOverTime(variable_names[name_index], node_index);
                assert ( time_series.size() == mpDataReader->GetUnlimitedDimensionValues().size());

                //fill the output_data data structure
                for (unsigned time_step = 0; time_step < time_series.size(); time_step++)
                {
                    output_data[time_step][requested_index] = time_series[time_step];
                }
            }
        }
        std::stringstream filename_stream;
        filename_stream << "NodalTraces_" << variable_names[name_index] << ".dat";
        WriteGenericFile(output_data, filename_stream.str());
    }
}


template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WriteGenericFile(std::vector<std::vector<double> >& rDataPayload, const std::string& rFileName)
{

    if(HeartConfig::Instance()->GetVisualizeWithMeshalyzer())
    {
        WriteGenericFileToMeshalyzer(rDataPayload, "output", rFileName);
    }
    if(HeartConfig::Instance()->GetVisualizeWithCmgui())
    {
        //Special case use of the wrong method - \todo #1660 need to change the format of this data
        WriteGenericFileToMeshalyzer(rDataPayload, "cmgui_output", rFileName);
    }


}
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WriteGenericFileToMeshalyzer(std::vector<std::vector<double> >& rDataPayload, const std::string& rFolder, const std::string& rFileName)
{
    OutputFileHandler output_file_handler(HeartConfig::Instance()->GetOutputDirectory() + "/" + rFolder, false);
    PetscTools::BeginRoundRobin();
    {
        out_stream p_file=out_stream(NULL);
        //Open file
        if (PetscTools::AmMaster())
        {
            //Open the file for the first time
            p_file = output_file_handler.OpenOutputFile(rFileName);
            //write provenance info
            std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
            *p_file << comment;
        }
        else
        {
            //Append to the existing file
            p_file = output_file_handler.OpenOutputFile(rFileName, std::ios::app);
        }
        //Write data
        for (unsigned line_number=0; line_number<rDataPayload.size(); line_number++)
        {
            for (unsigned i = 0; i < rDataPayload[line_number].size(); i++)
            {
                *p_file << rDataPayload[line_number][i] << "\t";
            }
            *p_file << std::endl;
        }
        p_file->close();
    }
    //There's a barrier included here: Process i+1 waits for process i to close the file
    PetscTools::EndRoundRobin();
}

// Explicit instantiation

template class PostProcessingWriter<1,1>;
template class PostProcessingWriter<1,2>;
template class PostProcessingWriter<2,2>;
template class PostProcessingWriter<1,3>;
template class PostProcessingWriter<3,3>;