RunAndCheckIonicModels.hpp

/*

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*/


#ifndef _RUNANDCHECKIONICMODELS_HPP_
#define _RUNANDCHECKIONICMODELS_HPP_

#include <vector>
#include <string>

#include "OdeSolution.hpp"

#include "ColumnDataWriter.hpp"
#include "ColumnDataReader.hpp"

#include "AbstractCardiacCell.hpp"
#include "HeartConfig.hpp"

void RunOdeSolverWithIonicModel(AbstractCardiacCellInterface* pOdeSystem,
                                double endTime,
                                std::string filename,
                                int stepPerRow=100,
                                bool doComputeExceptVoltage=true,
                                bool useSamplingInterval=false);

void CheckCellModelResults(const std::string& rBaseResultsFilename,
                           std::string validResultsBasename = "",
                           double tolerance = 1e-3,
                           std::string referenceFolder = "heart/test/data/ionicmodels");

std::vector<double> GetVoltages(ColumnDataReader& rReader);

void CompareCellModelResults(std::string baseResultsFilename1, std::string baseResultsFilename2,
                             double tolerance, bool vOnly=false, std::string folderName="TestIonicModels");


/*
 * Note: we have to have the function definitions here, rather than in a .cpp file, if we're
 * to include them in heart/src, as otherwise linking of the heart library fails because
 * CxxTest routines are not defined.
 */

#include <cmath>

void RunOdeSolverWithIonicModel(AbstractCardiacCellInterface* pOdeSystem,
                                double endTime,
                                std::string filename,
                                int stepPerRow,
                                bool doComputeExceptVoltage,
                                bool useSamplingInterval)
{
    double start_time = 0.0;

    if (doComputeExceptVoltage)
    {
        // Store the current system state
        std::vector<double> state_variables_copy = pOdeSystem->GetStdVecStateVariables();

        // Test ComputeExceptVoltage
        double v_init = pOdeSystem->GetVoltage();
        pOdeSystem->ComputeExceptVoltage(start_time, start_time + 100.0 /*ms*/);
        double v_end = pOdeSystem->GetVoltage();
        TS_ASSERT_DELTA(v_init, v_end, 1e-6);

        // Test SetVoltage
        pOdeSystem->SetVoltage(1e6);
        TS_ASSERT_DELTA(pOdeSystem->GetVoltage(), 1e6, 1e-6);

        // Reset the system
        pOdeSystem->SetStateVariables(state_variables_copy);
    }

    // Solve and write to file
    if (useSamplingInterval)
    {
        OdeSolution solution = pOdeSystem->Compute(start_time, endTime, HeartConfig::Instance()->GetOdeTimeStep() * stepPerRow);
        solution.WriteToFile("TestIonicModels", filename, "ms", 1, false, 4);
    }
    else
    {
        OdeSolution solution = pOdeSystem->Compute(start_time, endTime);
        solution.WriteToFile("TestIonicModels", filename, "ms", stepPerRow, false, 4);
    }
}

std::vector<double> GetVoltages(ColumnDataReader& rReader)
{
    //Rather Ugly, we can't currently guarantee what the name of the voltage column is,
    //hence we try to cover the most common possibilities
    std::vector<double> voltages;
    if (rReader.HasValues("V"))
    {
        voltages = rReader.GetValues("V");
    }
    else if (rReader.HasValues("membrane_voltage"))
    {
        voltages = rReader.GetValues("membrane_voltage");
    }
    else if (rReader.HasValues("membrane__V"))
    {
        voltages = rReader.GetValues("membrane__V");
    }
    else
    {
        EXCEPTION("Model membrane voltage not recognised.");
    }
    return voltages;
}

std::vector<double> GetIntracellularCalcium(ColumnDataReader& rReader)
{
    //Rather Ugly, we can't currently guarantee what the name of the calcium column is,
    //hence we try to cover the most common possibilities
    std::vector<double> cai;
    if (rReader.HasValues("CaI"))
    {
        cai = rReader.GetValues("CaI");
    }
    else if (rReader.HasValues("cytosolic_calcium_concentration"))
    {
        cai = rReader.GetValues("cytosolic_calcium_concentration");
    }
    else if (rReader.HasValues("Cai"))
    {
        cai = rReader.GetValues("Cai");
    }
    else
    {
        EXCEPTION("Model intracellular calcium is not recognised.");
    }
    return cai;
}

std::vector<double> GetHGate(ColumnDataReader& rReader)
{
    //Rather Ugly, we can't currently guarantee what the name of the h gate column is,
    //hence we try to cover the most common possibilities
    std::vector<double> h_values;
    if (rReader.HasValues("h"))
    {
        h_values = rReader.GetValues("h");
    }
    else if (rReader.HasValues("fast_sodium_current_h_gate__h"))
    {
        h_values = rReader.GetValues("fast_sodium_current_h_gate__h");
    }
    else if (rReader.HasValues("membrane_fast_sodium_current_h_gate"))
    {
        h_values = rReader.GetValues("membrane_fast_sodium_current_h_gate");
    }
    else
    {
        EXCEPTION("Model h gate is not recognised.");
    }
    return h_values;
}

/*
 * Check the cell model against a previous version
 * or another source e.g. Alan's COR
 */
void CheckCellModelResults(const std::string& rBaseResultsFilename,
                           std::string validResultsBasename,
                           double tolerance,
                           std::string referenceFolder)
{
    // read data entries for the new file
    ColumnDataReader data_reader("TestIonicModels", rBaseResultsFilename);
    std::vector<double> times = data_reader.GetValues("Time");
    std::vector<double> voltages = GetVoltages(data_reader);

    if (validResultsBasename == "")
    {
        validResultsBasename = rBaseResultsFilename;
    }

    ColumnDataReader valid_reader(referenceFolder, validResultsBasename + "ValidData",
                                  false);
    std::vector<double> valid_times = valid_reader.GetValues("Time");
    std::vector<double> valid_voltages = GetVoltages(valid_reader);

    TS_ASSERT_EQUALS(times.size(), valid_times.size());
    for (unsigned i=0; i<valid_times.size(); i++)
    {
        TS_ASSERT_DELTA(times[i], valid_times[i], 1e-12);
        TS_ASSERT_DELTA(voltages[i], valid_voltages[i], tolerance);
    }
}

void CompareCellModelResults(std::string baseResultsFilename1, std::string baseResultsFilename2,
                             double tolerance, bool vOnly, std::string folderName)
{
    // Compare 2 sets of results, e.g. from 2 different solvers for the same model.
    // If the time series differ, the finer resolution must be given first.
    ColumnDataReader data_reader1(folderName, baseResultsFilename1);
    std::vector<double> times1 = data_reader1.GetValues("Time");
    std::vector<double> voltages1 = GetVoltages(data_reader1);
    std::vector<double> calcium1;
    std::vector<double> h1;

    ColumnDataReader data_reader2(folderName, baseResultsFilename2);
    std::vector<double> times2 = data_reader2.GetValues("Time");
    std::vector<double> voltages2 = GetVoltages(data_reader2);
    std::vector<double> calcium2;
    std::vector<double> h2;

    if (!vOnly)
    {
        calcium1 = GetIntracellularCalcium(data_reader1);
        h1 = GetHGate(data_reader1);
        calcium2 = GetIntracellularCalcium(data_reader2);
        h2 = GetHGate(data_reader2);
    }

    TS_ASSERT(times1.size() >= times2.size());
    double last_v = voltages2[0];
    double tol = tolerance;
    for (unsigned i=0, j=0; i<times2.size(); i++)
    {
        // Find corresponding time index
        while (j<times1.size() && times1[j] < times2[i] - 1e-12)
        {
            j++;
        }

        // Set tolerance higher in upstroke
        if (fabs(voltages2[i] - last_v) > 0.05)
        {
            tol = tolerance * 25;
        }
        else
        {
            tol = tolerance;
        }
        last_v = voltages2[i];

        TS_ASSERT_DELTA(times1[j], times2[i], 1e-12);
        // adjust tol to data
        TS_ASSERT_DELTA(voltages1[j], voltages2[i], tol);
        if (!vOnly)
        {
            TS_ASSERT_DELTA(calcium1[j],  calcium2[i],  tol/100);
            TS_ASSERT_DELTA(h1[j],        h2[i],        tol/10);
        }
    }
}


#endif //_RUNANDCHECKIONICMODELS_HPP_