CellProperties.cpp

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#include <algorithm>
#include <cassert>
#include <cmath>
#include <sstream>

//#include <iostream>
//#include <iomanip>

#include "CellProperties.hpp"
#include "Exception.hpp"
#include "Warnings.hpp"

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.");
    }

    if (mrTime.size() != mrVoltage.size())
    {
        EXCEPTION("Time and Voltage series should be the same length. Time.size() = " << mrTime.size() << ", Voltage.size() = " << mrVoltage.size());
    }

    double max_upstroke_velocity = -DBL_MAX;
    double current_time_of_upstroke_velocity = 0;
    double current_resting_value = DBL_MAX;
    double current_peak = -DBL_MAX;
    double current_peak_time = -DBL_MAX;
    double current_minimum_velocity = DBL_MAX;
    double prev_voltage_derivative = 0;
    unsigned ap_counter = 0;
    unsigned counter_of_plateau_depolarisations = 0;
    //boolean to keep track whether we are switching phase from BELOWTHRESHOLD to ABOVETHRESHOLD
    bool switching_phase = false;
    bool found_a_flat_bit = false;
    APPhases ap_phase = BELOWTHRESHOLD;

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

    double v = mrVoltage[0];
    double t = mrTime[0];
    double prev_v = v;
    double prev_t = t;
    double voltage_derivative;
    const double resting_potential_gradient_threshold = 1e-2; 

    for (unsigned i = 1; i <= time_steps; i++)
    {
        v = mrVoltage[i];
        t = mrTime[i];
        voltage_derivative = (t == prev_t) ? 0.0 : (v - prev_v) / (t - prev_t);

        // Look for the max upstroke velocity and when it happens (could be below or above threshold).
        if (voltage_derivative >= max_upstroke_velocity)
        {
            max_upstroke_velocity = voltage_derivative;
            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 we can't find a flat bit, instead go for the minimum voltage
                //seen before the threshold.
                if (fabs(voltage_derivative) <= current_minimum_velocity && fabs(voltage_derivative) <= resting_potential_gradient_threshold)
                {
                    current_minimum_velocity = fabs(voltage_derivative);
                    current_resting_value = prev_v;
                    found_a_flat_bit = true;
                }
                else if (prev_v < current_resting_value && !found_a_flat_bit)
                {
                    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;
                    current_resting_value = 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]);
                    }

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

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

                // we check whether we have above threshold depolarisations
                // and only if if we haven't just switched from below threshold at this time step.
                // The latter is to avoid recording things depending on resting behaviour (in case of sudden upstroke from rest)
                if (prev_voltage_derivative <= 0 && voltage_derivative > 0 && !switching_phase)
                {
                    counter_of_plateau_depolarisations++;
                }

                // From the next time step, we are not "switching phase" any longer
                // (we want to check for above threshold deolarisations)
                switching_phase = false;

                // 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);
                    mTimesAtPeakValues.push_back(current_peak_time);
                    // Re-initialise the current_peak.
                    current_peak = mThreshold;
                    current_peak_time = -DBL_MAX;

                    // Register maximum upstroke velocity for this AP
                    mMaxUpstrokeVelocities.push_back(max_upstroke_velocity);
                    // Re-initialise max_upstroke_velocity
                    max_upstroke_velocity = -DBL_MAX;

                    // 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;

                    mCounterOfPlateauDepolarisations.push_back(counter_of_plateau_depolarisations);

                    //update the counters.
                    ap_counter++;
                    ap_phase = BELOWTHRESHOLD;

                    //reinitialise counter of plateau depolarisations
                    counter_of_plateau_depolarisations = 0;
                }
                break;
        }
        prev_v = v;
        prev_t = t;
        prev_voltage_derivative = voltage_derivative;
    }

    // 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(max_upstroke_velocity);
        mPeakValues.push_back(current_peak);
        mTimesAtPeakValues.push_back(current_peak_time);
        mTimesAtMaxUpstrokeVelocity.push_back(current_time_of_upstroke_velocity);
        mUnfinishedActionPotentials = true;
    }
}

std::vector<double> CellProperties::CalculateActionPotentialDurations(const double percentage)
{
    CheckExceededThreshold();

    double prev_v = mrVoltage[0];
    double prev_t = mrTime[0];
    std::vector<double> apds;
    std::vector<double> targets;
    double apd_start_time = DOUBLE_UNSET;
    double apd_end_time = DOUBLE_UNSET;

    unsigned apd_starting_index = UNSIGNED_UNSET;

    // New algorithm is to loop over APs instead of time.
    for (unsigned ap_index = 0; ap_index < mPeakValues.size(); ap_index++)
    {
        targets.push_back(mRestingValues[ap_index] + 0.01 * (100 - percentage) * (mPeakValues[ap_index] - mRestingValues[ap_index]));

        // We need to look from starting_time_index (just before threshold is reached)
        unsigned starting_time_index = std::lower_bound(mrTime.begin(), mrTime.end(), mOnsets[ap_index]) - mrTime.begin() - 1u;

        // Now if the target voltage for depolarisation is above the threshold,
        // we'll need to look forwards in time for the crossing point.
        if (targets[ap_index] >= mThreshold)
        {
            //std::cout << "Looking forwards\n";
            prev_v = mrVoltage[starting_time_index];
            prev_t = mrTime[starting_time_index];
            for (unsigned t = starting_time_index + 1u; t < mrTime.size(); t++)
            {
                if (mrVoltage[t] > targets[ap_index])
                {
                    apd_start_time = prev_t + ((targets[ap_index] - prev_v) / (mrVoltage[t] - prev_v)) * (mrTime[t] - prev_t);
                    apd_starting_index = t;
                    break;
                }
                prev_t = mrTime[t];
                prev_v = mrVoltage[t];
            }
        }
        else // otherwise, we'll need to look backwards.
        {
            //std::cout << "Looking backwards\n";
            prev_v = mrVoltage[starting_time_index + 1];
            prev_t = mrTime[starting_time_index + 1];
            for (int t = starting_time_index; t >= 0; t--)
            {
                if (mrVoltage[t] < targets[ap_index])
                {
                    apd_start_time = prev_t + ((targets[ap_index] - prev_v) / (mrVoltage[t] - prev_v)) * (mrTime[t] - prev_t);
                    apd_starting_index = (unsigned)(t + 1); // Should be a safe conversion since t not allowed to go negative in this loop.
                    break;
                }
                prev_t = mrTime[t];
                prev_v = mrVoltage[t];
            }
        }

        // If the start of this AP crossing threshold is before the last one finished,
        // we are in a wacky regime (see TestCellProperties::TestVeryLongApDetection() for examples of this)
        // and we need to skip the second one's evaluation.
        if (apd_end_time != DOUBLE_UNSET && apd_start_time != DOUBLE_UNSET && apd_start_time < apd_end_time)
        {
            continue; // Skip to next AP
        }

        // If there was a previous AP just check for common sense things (to help alert people to above situations)
        if (ap_index > 0u)
        {
            if (fabs(targets[ap_index] - targets[ap_index - 1u]) > 2) // If we see more than a 2mV shift in AP threshold
            {
                WARNING("The voltage threshold for measuring APD" << percentage << " changed from "
                                                                  << targets[ap_index - 1u] << " to " << targets[ap_index] << " in this AP trace, which may suggest CellProperties isn't telling you anything very sensible!");
            }
        }

        // Now just look forwards for the repolarisation time.
        if (apd_starting_index != UNSIGNED_UNSET)
        {
            prev_t = mrTime[apd_starting_index - 1u];
            prev_v = mrVoltage[apd_starting_index - 1u];
            // Now look for a fall below threshold after 1 past the Onset index
            for (unsigned t = apd_starting_index; t < mrTime.size(); t++)
            {
                if (mrVoltage[t] < targets[ap_index])
                {
                    apd_end_time = mrTime[t - 1] + ((targets[ap_index] - prev_v) / (mrVoltage[t] - prev_v)) * (mrTime[t] - mrTime[t - 1]);
                    apds.push_back(apd_end_time - apd_start_time);
                    break;
                }
                prev_t = mrTime[t];
                prev_v = mrVoltage[t];
            }
        }
    }

    if (apds.size() == 0)
    {
        EXCEPTION("No full action potential was recorded");
    }
    return apds;
}

std::vector<double> CellProperties::GetActionPotentialAmplitudes()
{
    CheckExceededThreshold();
    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::GetLastActionPotentialAmplitude()
{
    return GetActionPotentialAmplitudes().back();
}

void CellProperties::CheckExceededThreshold(void)
{
    // mOnsets and mRestingValues are all
    // set at the same time, so checking one should suffice.
    if (mOnsets.empty())
    {
        // possible false error here if the simulation started at time < 0
        EXCEPTION("AP did not occur, never exceeded threshold voltage.");
    }
}

void CellProperties::CheckReturnedToThreshold(void)
{
    // mPeakValues, mMaxUpstrokeVelocities and mTimesAtMaxUpstrokeVelocity are all
    // set at the same time so checking one should suffice.
    if (mMaxUpstrokeVelocities.empty())
    {
        EXCEPTION("AP did not occur, never descended past threshold voltage.");
    }
}

//
// The Get std::vector<double> methods
//

std::vector<double> CellProperties::GetCycleLengths()
{
    return mCycleLengths;
}

std::vector<double> CellProperties::GetRestingPotentials()
{
    CheckExceededThreshold();
    return mRestingValues;
}

std::vector<double> CellProperties::GetPeakPotentials()
{
    CheckReturnedToThreshold();
    return mPeakValues;
}

std::vector<double> CellProperties::GetTimesAtPeakPotentials()
{
    CheckReturnedToThreshold();
    return mTimesAtPeakValues;
}

std::vector<double> CellProperties::GetMaxUpstrokeVelocities()
{
    CheckReturnedToThreshold();
    return mMaxUpstrokeVelocities;
}

std::vector<double> CellProperties::GetTimesAtMaxUpstrokeVelocity()
{
    CheckReturnedToThreshold();
    return mTimesAtMaxUpstrokeVelocity;
}

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

std::vector<unsigned> CellProperties::GetNumberOfAboveThresholdDepolarisationsForAllAps()
{
    return mCounterOfPlateauDepolarisations;
}
//
// The Get <double> methods
//

double CellProperties::GetLastPeakPotential()
{
    CheckReturnedToThreshold();
    return mPeakValues.back();
}

double CellProperties::GetLastCompletePeakPotential()
{
    CheckReturnedToThreshold();
    double peak_value;
    if (mUnfinishedActionPotentials && mPeakValues.size() > 1u)
    {
        peak_value = mPeakValues[mPeakValues.size() - 2u];
    }
    else if (mUnfinishedActionPotentials && mPeakValues.size() == 1u)
    {
        EXCEPTION("No peak potential matching a full action potential was recorded.");
    }
    else
    {
        peak_value = mPeakValues.back();
    }
    return peak_value;
}

double CellProperties::GetTimeAtLastCompletePeakPotential()
{
    CheckReturnedToThreshold();
    double peak_value_time;
    if (mUnfinishedActionPotentials && mTimesAtPeakValues.size() > 1u)
    {
        peak_value_time = mTimesAtPeakValues[mTimesAtPeakValues.size() - 2u];
    }
    else if (mUnfinishedActionPotentials && mTimesAtPeakValues.size() == 1u)
    {
        EXCEPTION("No peak potential matching a full action potential was recorded.");
    }
    else
    {
        peak_value_time = mTimesAtPeakValues.back();
    }
    return peak_value_time;
}

double CellProperties::GetLastMaxUpstrokeVelocity()
{
    CheckReturnedToThreshold();
    return mMaxUpstrokeVelocities.back();
}

double CellProperties::GetLastCompleteMaxUpstrokeVelocity()
{
    CheckReturnedToThreshold();
    double max_upstroke;
    if (mUnfinishedActionPotentials && mMaxUpstrokeVelocities.size() > 1u)
    {
        max_upstroke = mMaxUpstrokeVelocities[mMaxUpstrokeVelocities.size() - 2u];
    }
    else if (mUnfinishedActionPotentials && mMaxUpstrokeVelocities.size() == 1u)
    {
        EXCEPTION("No MaxUpstrokeVelocity matching a full action potential was recorded.");
    }
    else
    {
        max_upstroke = mMaxUpstrokeVelocities.back();
    }
    return max_upstroke;
}

double CellProperties::GetTimeAtLastMaxUpstrokeVelocity()
{
    CheckReturnedToThreshold();
    return mTimesAtMaxUpstrokeVelocity.back();
}

double CellProperties::GetTimeAtLastPeakPotential()
{
    CheckReturnedToThreshold();
    return mTimesAtPeakValues.back();
}

double CellProperties::GetTimeAtLastCompleteMaxUpstrokeVelocity()
{
    CheckReturnedToThreshold();
    double max_upstroke_time;
    if (mUnfinishedActionPotentials && mTimesAtMaxUpstrokeVelocity.size() > 1u)
    {
        max_upstroke_time = mTimesAtMaxUpstrokeVelocity[mTimesAtMaxUpstrokeVelocity.size() - 2u];
    }
    else if (mUnfinishedActionPotentials && mTimesAtMaxUpstrokeVelocity.size() == 1u)
    {
        EXCEPTION("No TimeAtMaxUpstrokeVelocity matching a full action potential was recorded.");
    }
    else
    {
        max_upstroke_time = mTimesAtMaxUpstrokeVelocity.back();
    }
    return max_upstroke_time;
}

double CellProperties::GetLastActionPotentialDuration(const double percentage)
{
    // We tested this returns a non-empty vector in the method.
    return CalculateActionPotentialDurations(percentage).back();
}

unsigned CellProperties::GetNumberOfAboveThresholdDepolarisationsForLastAp()
{
    return mCounterOfPlateauDepolarisations.back();
}

double CellProperties::GetLastRestingPotential()
{
    // We tested something sensible has happened in the vector returning method.
    return GetRestingPotentials().back();
}