CellProperties.cpp

/*

Copyright (C) University of Oxford, 2005-2009

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.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/


#include "CellProperties.hpp"
#include "Exception.hpp"
#include <cmath>


enum APPhases { BELOWTHRESHOLD , ABOVETHRESHOLD };

void CellProperties::CalculateProperties()
{
    // Check we have some suitable data to process
    if (mrTime.size() < 1)
    {
        EXCEPTION("Insufficient time steps to calculate physiological properties.");
    }

    double prev_v = mrVoltage[0];
    double prev_t = mrTime[0];
    double current_upstroke_velocity = 0;
    double current_time_of_upstroke_velocity = 0;
    double current_resting_value=-DBL_MAX;
    double current_peak=-DBL_MAX;
    double current_minimum_velocity=DBL_MAX;
    double prev_upstroke_vel=0;
    unsigned ap_counter = 0;

    APPhases ap_phase = BELOWTHRESHOLD;

    unsigned time_steps = mrTime.size()-1; //The number of time steps is the number of intervals

    for (unsigned i=1; i<=time_steps; i++)
    {
        double v = mrVoltage[i];
        double t = mrTime[i];
        double upstroke_vel = (v - prev_v) / (t - prev_t);

        //Look for the upstroke velocity and when it happens (could be below or above threshold).
        if (upstroke_vel >= current_upstroke_velocity)
        {
            current_upstroke_velocity = upstroke_vel;
            current_time_of_upstroke_velocity = t;
        }

        switch (ap_phase)
        {
            case BELOWTHRESHOLD:
                //while below threshold, find the resting value by checking where the velocity is minimal
                //i.e. when it is flattest
                if (fabs(upstroke_vel)<=current_minimum_velocity)
                {
                    current_minimum_velocity=fabs(upstroke_vel);
                    current_resting_value = prev_v;
                }

                // If we cross the threshold, this counts as an AP
                if ( v>mThreshold && prev_v <= mThreshold )
                {
                    //register the resting value and re-initialise the minimum velocity
                    mRestingValues.push_back(current_resting_value);
                    current_minimum_velocity = DBL_MAX;

                    //Register the onset time. Linear interpolation.
                    mOnsets.push_back(prev_t + (t-prev_t)/(v-prev_v)*(mThreshold-prev_v));

                    //If it is not the first AP, calculate cycle length for the last two APs
                    if (ap_counter>0)
                    {
                        mCycleLengths.push_back( mOnsets[ap_counter]-mOnsets[ap_counter-1] );
                    }

                    ap_phase = ABOVETHRESHOLD;
                    // no break here - deliberate fall through to next case
                }
                else
                {
                    break;
                }

            case ABOVETHRESHOLD:
                //While above threshold, look for the peak potential for the current AP
                if (v>current_peak)
                {
                   current_peak = v;
                }

                // If we cross the threshold again, the AP is over
                // and we register all the parameters.
                if ( v<mThreshold && prev_v >= mThreshold )
                {
                    //register peak value for this AP
                    mPeakValues.push_back(current_peak);
                    //Re-initialise the current_peak.
                    current_peak = mThreshold;

                    //register maximum upstroke velocity for this AP
                    mMaxUpstrokeVelocities.push_back(current_upstroke_velocity);
                    //re-initialise current_upstroke_velocity
                    current_upstroke_velocity = 0.0;

                    //register time when maximum upstroke velocity occurred for this AP
                    mTimesAtMaxUpstrokeVelocity.push_back(current_time_of_upstroke_velocity);
                    //re-initialise current_time_of_upstroke_velocity=t;
                    current_time_of_upstroke_velocity = 0.0;

                    //update the counter.
                    ap_counter++;
                    ap_phase = BELOWTHRESHOLD;
                }
                break;
        }

        prev_v = v;
        prev_t = t;
        prev_upstroke_vel = upstroke_vel;
    }

    // One last check. If the simulation ends halfway through an AP
    // i.e. if the vectors of onsets has more elements than the vectors
    // of peak and upstroke properties (that are updated at the end of the AP),
    // then we register the peak and upstroke values so far
    // for the last incomplete AP.
    if (mOnsets.size()>mMaxUpstrokeVelocities.size())
    {
        mMaxUpstrokeVelocities.push_back(current_upstroke_velocity);
    }
    if (mOnsets.size()>mPeakValues.size())
    {
        mPeakValues.push_back(current_peak);
    }
    if (mOnsets.size()>mTimesAtMaxUpstrokeVelocity.size())
    {
        mTimesAtMaxUpstrokeVelocity.push_back(current_time_of_upstroke_velocity);
    }
}


std::vector<double> CellProperties::CalculateActionPotentialDurations(const double percentage)
{
    if (mOnsets.size() == 0)
    {
        // possible false error here if the simulation started at time < 0
        EXCEPTION("No upstroke occurred");
    }

    double prev_v = -DBL_MAX;
    unsigned APcounter=0;//will keep count of the APDs that we calculate
    bool apd_is_calculated=true;//this will ensure we hit the target only once per AP.
    std::vector<double> apds;
    double target = DBL_MAX;
    
    for (unsigned i=0; i<mrTime.size(); i++)
    {
        double t = mrTime[i];
        double v = mrVoltage[i];

        //First we make sure we stop calculating after the last AP has been calculated
        if (APcounter<mPeakValues.size())
        {
            //Set the target potential
            target = mRestingValues[APcounter]+0.01*(100-percentage)*(mPeakValues[APcounter]-mRestingValues[APcounter]);

            //if we reach the peak, we need to start to calculate an APD
            if (fabs(v-mPeakValues[APcounter])<=1e-6)
            {
                apd_is_calculated = false;
            }
            //if we hit the target while repolarising
            //and we are told this apd is not calculated yet.
            if ( prev_v>v && prev_v>=target && v<=target && apd_is_calculated==false)
            {
                apds.push_back (t - mOnsets[APcounter]); 
                APcounter++;
                apd_is_calculated = true;
            }
        }
        prev_v = v;
    }
    if (apds.size() == 0)
    {
        EXCEPTION("No full action potential was recorded");
    }
    return apds;
}


std::vector<double> CellProperties::GetAllActionPotentialDurations(const double percentage)
{
    return CalculateActionPotentialDurations(percentage);
}

double CellProperties::GetLastActionPotentialDuration(const double percentage)
{
     std::vector<double> apds = CalculateActionPotentialDurations(percentage);

    //return the last apd
    return apds[apds.size()-1];
}

std::vector<double> CellProperties::GetActionPotentialAmplitudes()
{
    unsigned size = mPeakValues.size();
    std::vector<double> amplitudes(size);
    for (unsigned i=0; i< size ;i++)
    {
        amplitudes[i] = (mPeakValues[i] - mRestingValues[i]);
    }
    return amplitudes;
}
double CellProperties::GetLastMaxUpstrokeVelocity()
{
    unsigned size = mMaxUpstrokeVelocities.size();
    if (size==0)
    {
        EXCEPTION("Upstroke never occurred");
    }
    return mMaxUpstrokeVelocities[size-1];

}
double CellProperties::GetTimeAtLastMaxUpstrokeVelocity()
{
    unsigned size = mTimesAtMaxUpstrokeVelocity.size();
    if (size==0)
    {
        EXCEPTION("Upstroke never occurred");
    }
    return mTimesAtMaxUpstrokeVelocity[size-1];
}

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