RunAndCheckIonicModels.hpp

/*

Copyright (c) 2005-2017, University of Oxford.
All rights reserved.

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/


#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_