PropagationPropertiesCalculator.cpp

/*

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#include "UblasIncludes.hpp"
#include "PropagationPropertiesCalculator.hpp"
#include "CellProperties.hpp"
#include "Exception.hpp"
#include <sstream>
#include "HeartEventHandler.hpp"

PropagationPropertiesCalculator::PropagationPropertiesCalculator(Hdf5DataReader* pDataReader,
                                                                 const std::string voltageName)
    : mpDataReader(pDataReader),
      mVoltageName(voltageName),
      mTimes(mpDataReader->GetUnlimitedDimensionValues()),
      mCachedNodeGlobalIndex(UNSIGNED_UNSET)
{}

PropagationPropertiesCalculator::~PropagationPropertiesCalculator()
{
    // We don't own the data reader, so we don't destroy it.
}

double PropagationPropertiesCalculator::CalculateMaximumUpstrokeVelocity(unsigned globalNodeIndex)
{
    std::vector<double>& r_voltages = rGetCachedVoltages(globalNodeIndex);
    CellProperties cell_props(r_voltages, mTimes);
    return cell_props.GetLastMaxUpstrokeVelocity();
}

std::vector<double> PropagationPropertiesCalculator::CalculateAllMaximumUpstrokeVelocities(unsigned globalNodeIndex, double threshold)
{
    std::vector<double>& r_voltages = rGetCachedVoltages(globalNodeIndex);
    CellProperties cell_props(r_voltages, mTimes, threshold);
    return cell_props.GetMaxUpstrokeVelocities();
}

std::vector<double> PropagationPropertiesCalculator::CalculateUpstrokeTimes(unsigned globalNodeIndex, double threshold)
{
    std::vector<double>& r_voltages = rGetCachedVoltages(globalNodeIndex);
    CellProperties cell_props(r_voltages, mTimes, threshold);
    return cell_props.GetTimesAtMaxUpstrokeVelocity();
}

double PropagationPropertiesCalculator::CalculateActionPotentialDuration(const double percentage,
                                                                         unsigned globalNodeIndex)
{
    if (percentage < 1.0 || percentage >= 100.0)
    {
        EXCEPTION("First argument of CalculateActionPotentialDuration() is expected to be a percentage");
    }
    std::vector<double>& r_voltages = rGetCachedVoltages(globalNodeIndex);
    CellProperties cell_props(r_voltages, mTimes);
    return cell_props.GetLastActionPotentialDuration(percentage);
}

std::vector<double> PropagationPropertiesCalculator::CalculateAllActionPotentialDurations(const double percentage,
                                                                                          unsigned globalNodeIndex,
                                                                                          double threshold)
{
    std::vector<double>& r_voltages = rGetCachedVoltages(globalNodeIndex);
    CellProperties cell_props(r_voltages, mTimes, threshold);
    return cell_props.GetAllActionPotentialDurations(percentage);
}

std::vector<std::vector<double> > PropagationPropertiesCalculator::CalculateAllActionPotentialDurationsForNodeRange(
        const double percentage,
        unsigned lowerNodeIndex,
        unsigned upperNodeIndex,
        double threshold)
{
    std::vector<std::vector<double> > output_data;
    output_data.reserve(upperNodeIndex-lowerNodeIndex+1);
    unsigned num_nodes_per_data_block = 100; // number of nodes
    unsigned num_complete_blocks = (upperNodeIndex-lowerNodeIndex) / num_nodes_per_data_block;
    unsigned size_last_block = (upperNodeIndex-lowerNodeIndex) % num_nodes_per_data_block;

    for (unsigned block_num=0;
         block_num<num_complete_blocks+1;
         block_num++)
    {
        unsigned num_nodes_to_read;
        if (block_num != num_complete_blocks)
        {
            num_nodes_to_read = num_nodes_per_data_block;
        }
        else
        {
            num_nodes_to_read = size_last_block;
        }

        if (num_nodes_to_read > 0)
        {
            // Read a big block of data
            unsigned low_node = lowerNodeIndex + block_num*num_nodes_per_data_block;
            unsigned high_node = low_node + num_nodes_to_read;
            std::vector<std::vector<double> > voltages = mpDataReader->GetVariableOverTimeOverMultipleNodes(mVoltageName, low_node, high_node);

            for (unsigned node_within_block=0;
                 node_within_block < num_nodes_to_read;
                 node_within_block++)
            {
                std::vector<double>& r_voltages = voltages[node_within_block];
                CellProperties cell_props(r_voltages, mTimes, threshold);
                std::vector<double> apds;
                try
                {
                    apds = cell_props.GetAllActionPotentialDurations(percentage);
                    assert(apds.size() != 0);
                }
                catch (Exception& e)
                {
                    assert(e.GetShortMessage()=="No full action potential was recorded" ||
                           e.GetShortMessage()=="AP did not occur, never exceeded threshold voltage.");
                    apds.push_back(0);
                    assert(apds.size() == 1);
                }
                output_data.push_back(apds);
            }
        }
    }
    return output_data;
}

double PropagationPropertiesCalculator::CalculatePeakMembranePotential(unsigned globalNodeIndex)
{
    std::vector<double>& r_voltages = rGetCachedVoltages(globalNodeIndex);
    double max = -DBL_MAX;
    for (unsigned i=0; i<r_voltages.size(); i++)
    {
        if (r_voltages[i]>max)
        {
            max = r_voltages[i];
        }
    }
    return max;
}

double PropagationPropertiesCalculator::CalculateConductionVelocity(unsigned globalNearNodeIndex,
                                                                    unsigned globalFarNodeIndex,
                                                                    const double euclideanDistance)
{
    double t_near = 0;
    double t_far = 0;
    std::vector<double>& r_near_voltages = rGetCachedVoltages(globalNearNodeIndex);
    std::vector<double> far_voltages = mpDataReader->GetVariableOverTime(mVoltageName, globalFarNodeIndex);

    CellProperties near_cell_props(r_near_voltages, mTimes);
    CellProperties far_cell_props(far_voltages, mTimes);

    //The size of each vector is the number of APs that reached that node
    unsigned aps_near_node = near_cell_props.GetMaxUpstrokeVelocities().size();
    unsigned aps_far_node = far_cell_props.GetMaxUpstrokeVelocities().size();

    //These should never be empty. If so, an exception should have been thrown in the GetMaxUpstrokeVelocities() method.
    assert(aps_near_node > 0);
    assert(aps_far_node > 0);

    //if the same number of APs reached both nodes, get the last one...
    if (aps_near_node == aps_far_node)
    {
        t_near = near_cell_props.GetTimeAtLastMaxUpstrokeVelocity();
        t_far = far_cell_props.GetTimeAtLastMaxUpstrokeVelocity();
    }
    //...otherwise get the one with the smallest value, which is the last AP to reach both nodes
    //This prevents possible calculation of negative conduction velocities
    //for repeated stimuli
    else if (aps_near_node > aps_far_node)
    {
        t_near = near_cell_props.GetTimesAtMaxUpstrokeVelocity()[aps_far_node-1];
        t_far = far_cell_props.GetTimesAtMaxUpstrokeVelocity()[aps_far_node-1];
    }
    else
    {
        t_near = near_cell_props.GetTimesAtMaxUpstrokeVelocity()[aps_near_node-1];
        t_far = far_cell_props.GetTimesAtMaxUpstrokeVelocity()[aps_near_node-1];
    }

    if ((globalNearNodeIndex == globalFarNodeIndex) || ( fabs(t_far - t_near) < 1e-8))
    {
        // globalNearNodeIndex and globalFarNodeIndex are the same node, preventing a 0/0
        // or
        // AP number i is happening at the same time at nodes globalNearNodeIndex and globalFarNodeIndex
        return 0.0;
    }
    else
    {
        return euclideanDistance / (t_far - t_near);
    }


}

std::vector<double> PropagationPropertiesCalculator::CalculateAllConductionVelocities(unsigned globalNearNodeIndex,
                                                                                      unsigned globalFarNodeIndex,
                                                                                      const double euclideanDistance)
{
    std::vector<double> conduction_velocities;

    std::vector<double> t_near;
    std::vector<double> t_far;
    unsigned number_of_aps = 0;

    std::vector<double>& r_near_voltages = rGetCachedVoltages(globalNearNodeIndex);
    std::vector<double> far_voltages = mpDataReader->GetVariableOverTime(mVoltageName, globalFarNodeIndex);

    CellProperties near_cell_props(r_near_voltages, mTimes);
    CellProperties far_cell_props(far_voltages, mTimes);

    t_near = near_cell_props.GetTimesAtMaxUpstrokeVelocity();
    t_far = far_cell_props.GetTimesAtMaxUpstrokeVelocity();

    //exception should have been thrown within the GetTimesAtMaxUpstrokeVelocity method if the threshold is never reached
    //and these vectors are empty
    assert(t_near.size() !=0);
    assert(t_far.size() !=0);

    //Check the node where the least number of aps is reached.
    //We will calculate only where AP reached both nodes
    if (t_near.size() > t_far.size())
    {
        number_of_aps = t_far.size();
    }
    else
    {
        number_of_aps = t_near.size();
    }
    //now fill the vector

    if (globalNearNodeIndex == globalFarNodeIndex)
    {
        // globalNearNodeIndex and globalFarNodeIndex are the same node, preventing a 0/0
        for (unsigned i = 0 ; i < number_of_aps;i++)
        {
            conduction_velocities.push_back(0.0);
        }
    }
    else
    {
        for (unsigned i = 0 ; i < number_of_aps;i++)
        {
            if ( fabs(t_far[i] - t_near[i]) < 1e-8)
            {
                // AP number i is happening at the same time at nodes globalNearNodeIndex and globalFarNodeIndex
                conduction_velocities.push_back(0.0);
            }
            else
            {
                conduction_velocities.push_back(euclideanDistance / (t_far[i] - t_near[i]));
            }
        }
    }

    return conduction_velocities;
}


std::vector<unsigned> PropagationPropertiesCalculator::CalculateAllAboveThresholdDepolarisations(unsigned globalNodeIndex, double threshold)
{
    std::vector<double>& r_voltages = rGetCachedVoltages(globalNodeIndex);
    CellProperties cell_props(r_voltages, mTimes, threshold);
    return cell_props.GetNumberOfAboveThresholdDepolarisationsForAllAps();
}


unsigned PropagationPropertiesCalculator::CalculateAboveThresholdDepolarisationsForLastAp(unsigned globalNodeIndex, double threshold)
{
    std::vector<double>& r_voltages = rGetCachedVoltages(globalNodeIndex);
    CellProperties cell_props(r_voltages, mTimes, threshold);
    return cell_props.GetNumberOfAboveThresholdDepolarisationsForLastAp();
}


std::vector<double>& PropagationPropertiesCalculator::rGetCachedVoltages(unsigned globalNodeIndex)
{
    if (globalNodeIndex != mCachedNodeGlobalIndex)
    {
        mCachedVoltages = mpDataReader->GetVariableOverTime(mVoltageName, globalNodeIndex);
        mCachedNodeGlobalIndex = globalNodeIndex;
    }
    return mCachedVoltages;
}