PropagationPropertiesCalculator.cpp

/*

Copyright (C) University of Oxford, 2005-2011

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 "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 = rCacheVoltages(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 = rCacheVoltages(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 = rCacheVoltages(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 = rCacheVoltages(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 = rCacheVoltages(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 = rCacheVoltages(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 = rCacheVoltages(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 = rCacheVoltages(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 = rCacheVoltages(globalNodeIndex);
    CellProperties cell_props(r_voltages, mTimes, threshold);
    return cell_props.GetNumberOfAboveThresholdDepolarisationsForAllAps();
}


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


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