AbstractCvodeCellWithDataClamp.cpp

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#ifdef CHASTE_CVODE

#include <sstream>
#include <iostream>
#include <cmath>

#include "AbstractCvodeCellWithDataClamp.hpp"
#include "Exception.hpp"
#include "HeartConfig.hpp"
#include "VectorHelperFunctions.hpp"
#include <algorithm>


AbstractCvodeCellWithDataClamp::AbstractCvodeCellWithDataClamp(boost::shared_ptr<AbstractIvpOdeSolver> pSolver/* unused */,
                                                               unsigned numberOfStateVariables,
                                                               unsigned voltageIndex,
                                                               boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus)
    : AbstractCvodeCell(pSolver, numberOfStateVariables, voltageIndex, pIntracellularStimulus),
      mDataAvailable(false),
      mDataClampIsOn(false)
{
}

AbstractCvodeCellWithDataClamp::~AbstractCvodeCellWithDataClamp()
{
}

void AbstractCvodeCellWithDataClamp::SetExperimentalData(std::vector<double> experimentalTimes,
                                                         std::vector<double> experimentalVoltages)
{
    assert(experimentalVoltages.size()==experimentalTimes.size());
    assert(experimentalVoltages.size()>1u);
    mExperimentalTimes = experimentalTimes;
    mExperimentalVoltages = experimentalVoltages;
    mDataAvailable = true;
}

double AbstractCvodeCellWithDataClamp::GetExperimentalVoltageAtTimeT(const double& rTime) // Linearly interpolate between data points
{
    if (!mDataClampIsOn)
    {
        // For speed we want to be able to skip this method.
        return DOUBLE_UNSET;
    }

    if (rTime > mExperimentalTimes.back() || rTime < mExperimentalTimes[0])
    {
        EXCEPTION("The requested time " << rTime << " is outside the times stored in the data clamp.");
    }

    std::vector<double>::iterator upper_vec =
            std::upper_bound(mExperimentalTimes.begin(), mExperimentalTimes.end(), rTime);
    // upper_vec points to first element that is (strictly) > rTime (so it can't be first one if rTime is in range)

    // Special case - here the lower bound is equal to upper bound and both are pointing to end!
    if (upper_vec == mExperimentalTimes.end())
    {
        return mExperimentalVoltages.back();
    }

    unsigned upper_index = upper_vec - mExperimentalTimes.begin();

    assert(upper_index>0u); // Sanity check to avoid seg faults below.
    // if this assert ever fails we may need the code below, but I can't see how it could!
//    if (upper_index == 0u)
//    {
//        // Special case - here the lower bound is equal to upper bound and no interpolation needed
//        return mExperimentalVoltages[0];
//    }

    double lower_time = mExperimentalTimes[upper_index-1];
    double increment = rTime - lower_time;
    double time_step = mExperimentalTimes[upper_index] - mExperimentalTimes[upper_index-1];
    double voltage_step = mExperimentalVoltages[upper_index] - mExperimentalVoltages[upper_index-1];
    return mExperimentalVoltages[upper_index-1] + increment * voltage_step / time_step;
}

void AbstractCvodeCellWithDataClamp::TurnOffDataClamp()
{
    this->SetParameter("membrane_data_clamp_current_conductance",0);
    mDataClampIsOn = false;
}

void AbstractCvodeCellWithDataClamp::TurnOnDataClamp(double conductance)
{
    if (!mDataAvailable)
    {
        EXCEPTION("Before calling TurnOnDataClamp(), please provide experimental data via the SetExperimentalData() method.");
    }
    assert(mExperimentalTimes.size() > 1u);
    this->SetParameter("membrane_data_clamp_current_conductance", conductance);
    mDataClampIsOn = true;
}

#endif // CHASTE_CVODEWITHDATACLAMP