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 "Hdf5DataWriter.hpp"
 
#include <iostream>
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::PostProcessingWriter(AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>& rMesh,
                                                                   const FileFinder& rDirectory,
                                                                   const std::string& rHdf5FileName,
                                                                   const std::string& rVoltageName,
                                                                   hsize_t hdf5DataWriterChunkSize)
        : mDirectory(rDirectory),
          mHdf5File(rHdf5FileName),
          mVoltageName(rVoltageName),
          mrMesh(rMesh),
          mHdf5DataWriterChunkSize(hdf5DataWriterChunkSize)
{
    mLo = mrMesh.GetDistributedVectorFactory()->GetLow();
    mHi = mrMesh.GetDistributedVectorFactory()->GetHigh();
    mpDataReader = new Hdf5DataReader(mDirectory, mHdf5File);
    mpCalculator = new PropagationPropertiesCalculator(mpDataReader, mVoltageName);
    // Check that the hdf file was generated by simulations from (probably) 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());
 
    // 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);
 
        delete mpDataReader;
 
        for (unsigned i=0; i<electrodes.size(); i++)
        {
            PseudoEcgCalculator<ELEMENT_DIM,SPACE_DIM,1> calculator(mrMesh,
                                                                    electrodes[i],
                                                                    mDirectory,
                                                                    mHdf5File,
                                                                    mVoltageName);
            calculator.WritePseudoEcg();
        }
 
        mpDataReader = new Hdf5DataReader(mDirectory, mHdf5File);
        mpCalculator->SetHdf5DataReader(mpDataReader);
    }
}
 
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>::WriteOutputDataToHdf5(const std::vector<std::vector<double> >& rDataPayload,
                                                                         const std::string& rDatasetName,
                                                                         const std::string& rDatasetUnit,
                                                                         const std::string& rUnlimitedVariableName,
                                                                         const std::string& rUnlimitedVariableUnit)
{
    DistributedVectorFactory* p_factory = mrMesh.GetDistributedVectorFactory();
    FileFinder test_output("", RelativeTo::ChasteTestOutput);
    Hdf5DataWriter writer(*p_factory,
                          mDirectory.GetRelativePath(test_output),  // Path relative to CHASTE_TEST_OUTPUT
                          mHdf5File,
                          false, // to wiping
                          true,  // to extending
                          rDatasetName); // dataset name
 
    /* Probe define mode. We asked to extend, so if the writer is currently in define mode it means the
     * dataset doesn't exist yet and needs creating. If it is NOT in define mode, it means the dataset
     * exists, so we'll empty it and calculate new postprocessing data. */
    int apd_id;
    if (writer.IsInDefineMode())
    {
        apd_id = writer.DefineVariable(rDatasetName, rDatasetUnit);
        writer.DefineFixedDimension(mrMesh.GetNumNodes());
        writer.DefineUnlimitedDimension(rUnlimitedVariableName, rUnlimitedVariableUnit);
        if (mHdf5DataWriterChunkSize>0u)
        {
            /* Pass target chunk size through to writer. (We don't do the
             * alignment one as well because that can only be done for a new
             * file and PostProcessingWriter can only add to an existing file.)
             */
            writer.SetTargetChunkSize(mHdf5DataWriterChunkSize);
        }
        writer.EndDefineMode();
    }
    else
    {
        apd_id = writer.GetVariableByName(rDatasetName);
        writer.EmptyDataset();
    }
 
    //Determine the maximum number of paces
    unsigned local_max_paces = 0u;
    for (unsigned node_index = 0; node_index < rDataPayload.size(); ++node_index)
    {
        if (rDataPayload[node_index].size() > local_max_paces)
        {
             local_max_paces = rDataPayload[node_index].size();
        }
    }
 
    unsigned max_paces = 0u;
    MPI_Allreduce(&local_max_paces, &max_paces, 1, MPI_UNSIGNED, MPI_MAX, PETSC_COMM_WORLD);
 
    for (unsigned pace_idx = 0; pace_idx < max_paces; pace_idx++)
    {
        Vec apd_vec = p_factory->CreateVec();
        DistributedVector distributed_vector = p_factory->CreateDistributedVector(apd_vec);
        for (DistributedVector::Iterator index = distributed_vector.Begin();
             index!= distributed_vector.End();
             ++index)
        {
            unsigned node_idx = index.Local;
            // pad with -999 if no pace defined at this node
            if (pace_idx < rDataPayload[node_idx].size() )
            {
                distributed_vector[index] = rDataPayload[node_idx][pace_idx];
            }
            else
            {
                distributed_vector[index] = -999.0;
            }
        }
        writer.PutVector(apd_id, apd_vec);
        PetscTools::Destroy(apd_vec);
        writer.PutUnlimitedVariable(pace_idx);
        writer.AdvanceAlongUnlimitedDimension();
    }
    writer.Close();
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::WriteApdMapFile(double repolarisationPercentage, double threshold)
{
    std::vector<std::vector<double> > local_output_data = mpCalculator->CalculateAllActionPotentialDurationsForNodeRange(repolarisationPercentage, mLo, mHi, threshold);
 
    // HDF5 shouldn't have minus signs in the data names..
    std::stringstream hdf5_dataset_name;
    hdf5_dataset_name << "Apd_" << repolarisationPercentage;
 
    WriteOutputDataToHdf5(local_output_data,
                          hdf5_dataset_name.str() + ConvertToHdf5FriendlyString(threshold) + "_Map",
                          "msec");
}
 
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&)
        {
            upstroke_times.push_back(0);
            assert(upstroke_times.size() == 1);
        }
        output_data.push_back(upstroke_times);
    }
 
    WriteOutputDataToHdf5(output_data,
                          "UpstrokeTimeMap" + ConvertToHdf5FriendlyString(threshold),
                          "msec");
}
 
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&)
        {
            upstroke_velocities.push_back(0);
            assert(upstroke_velocities.size() ==1);
        }
        output_data.push_back(upstroke_velocities);
    }
 
    WriteOutputDataToHdf5(output_data,
                          "MaxUpstrokeVelocityMap" + ConvertToHdf5FriendlyString(threshold),
                          "mV_per_msec");
}
 
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&)
        {
            conduction_velocities.push_back(0);
            assert(conduction_velocities.size() == 1);
        }
        output_data.push_back(conduction_velocities);
    }
    std::stringstream filename_stream;
    filename_stream << "ConductionVelocityFromNode" << originNode;
 
    WriteOutputDataToHdf5(output_data, filename_stream.str(), "cm_per_msec");
}
 
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&)
        {
            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((double)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);
    }
 
    // we just use meshalyzer format so that something is generated in simple column format for use with gnuplot etc.
    WriteGenericFileToMeshalyzer(output_data, "", "AboveThresholdDepolarisations" + ConvertToHdf5FriendlyString(threshold) +
                                 ".dat");
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::string PostProcessingWriter<ELEMENT_DIM, SPACE_DIM>::ConvertToHdf5FriendlyString(double threshold)
{
    std::stringstream dataset_stream;
    std::string extra_message = "_";
    if (threshold < 0.0)
    {
        extra_message += "minus_";
        threshold = -threshold;
    }
 
    // if threshold is a decimal eg: because using phenomenological model
    if (threshold - floor(threshold) > 1e-8)
    {
        // give the answer to 2dp
        dataset_stream << extra_message << floor(threshold) << "pt" << floor(threshold*100)-(floor(threshold)*100);
    }
    else
    {
        dataset_stream << extra_message << threshold;
    }
 
    return dataset_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";
        // we just use meshalyzer format so that something is generated in simple column format for use with gnuplot etc.
        WriteGenericFileToMeshalyzer(output_data, "", filename_stream.str());
    }
}
 
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);
        }
        else
        {
            // Append data to the existing file opened by master
            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;
        }
 
        // Last processor appends comment line
        if (PetscTools::AmTopMost())
        {
            std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
            *p_file << comment;
        }
        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>;