WaveformTools_tool.cc

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////////////////////////////////////////////////////////////////////////
/// \file   WaveformTools_tool.cc
/// \author T. Usher
////////////////////////////////////////////////////////////////////////

#include <cmath>
#include <numeric> // std::inner_product
#include "larreco/HitFinder/HitFinderTools/IWaveformTool.h"
#include "art/Utilities/ToolMacros.h"

#include "TProfile.h"
#include "TVirtualFFT.h"

namespace reco_tool
{

class WaveformTools : IWaveformTool
{
public:
    explicit WaveformTools(const fhicl::ParameterSet& pset);

    ~WaveformTools() {}

    void configure(const fhicl::ParameterSet& pset)  override;

    using PeakTuple    = std::tuple<size_t,size_t,size_t>; // first bin, peak bin, last bin
    using PeakTupleVec = std::vector<PeakTuple>;

    void triangleSmooth(const std::vector<float>&,  std::vector<float>&,  size_t = 0)                           const override;
    void triangleSmooth(const std::vector<double>&, std::vector<double>&, size_t = 0)                           const override;
    void medianSmooth(  const std::vector<float>&,  std::vector<float>&,  size_t = 3)                           const override;
    void medianSmooth(  const std::vector<double>&, std::vector<double>&, size_t = 3)                           const override;
    void getTruncatedMeanRMS(const std::vector<double>&, double&, double&, double&, int&)                       const override;
    void getTruncatedMeanRMS(const std::vector<float>&, float&, float&, float&, int&)                           const override;
    void firstDerivative(const std::vector<float>&,  std::vector<float>&)                                       const override;
    void firstDerivative(const std::vector<double>&, std::vector<double>&)                                      const override;
    void findPeaks(std::vector<float>::iterator,  std::vector<float>::iterator,  PeakTupleVec&, float, size_t)  const override;
    void findPeaks(std::vector<double>::iterator, std::vector<double>::iterator, PeakTupleVec&, double, size_t) const override;
    void getFFTPower(const std::vector<float>& inputVec, std::vector<float>& outputPowerVec)                    const override;
    void getFFTPower(const std::vector<double>& inputVec, std::vector<double>& outputPowerVec)                  const override;

    void getErosionDilationAverageDifference(const Waveform<short>&,
                                             int,
                                             HistogramMap&,
                                             Waveform<short>&,
                                             Waveform<short>&,
                                             Waveform<short>&,
                                             Waveform<short>&)         const override;
    void getErosionDilationAverageDifference(const Waveform<float>&,
                                             int,
                                             HistogramMap&,
                                             Waveform<float>&,
                                             Waveform<float>&,
                                             Waveform<float>&,
                                             Waveform<float>&)         const override;
    void getErosionDilationAverageDifference(const Waveform<double>&,
                                             int,
                                             HistogramMap&,
                                             Waveform<double>&,
                                             Waveform<double>&,
                                             Waveform<double>&,
                                             Waveform<double>&)         const override;

    void getOpeningAndClosing(const Waveform<short>&,  const Waveform<short>&,  int, HistogramMap&, Waveform<short>&,  Waveform<short>&)  const override;
    void getOpeningAndClosing(const Waveform<float>&,  const Waveform<float>&,  int, HistogramMap&, Waveform<float>&,  Waveform<float>&)  const override;
    void getOpeningAndClosing(const Waveform<double>&, const Waveform<double>&, int, HistogramMap&, Waveform<double>&, Waveform<double>&) const override;

private:
    template <typename T> void triangleSmooth(const std::vector<T>&, std::vector<T>&, size_t = 0)                                        const;
    template <typename T> void medianSmooth(  const std::vector<T>&, std::vector<T>&, size_t = 3)                                        const;
    template <typename T> void getTruncatedMeanRMS(const std::vector<T>&, T&, T&, T&, int&)                                              const;
    template <typename T> void firstDerivative(const std::vector<T>&,  std::vector<T>&)                                                  const;
    template <typename T> void findPeaks(typename std::vector<T>::iterator, typename std::vector<T>::iterator, PeakTupleVec&, T, size_t) const;

    template <typename T> void getErosionDilationAverageDifference(const Waveform<T>&,
                                                                   int,
                                                                   HistogramMap&,
                                                                   Waveform<T>&,
                                                                   Waveform<T>&,
                                                                   Waveform<T>&,
                                                                   Waveform<T>&) const;

    template <typename T> void getOpeningAndClosing(const Waveform<T>&,  const Waveform<T>&,  int, HistogramMap&, Waveform<T>&,  Waveform<T>&)  const;
};

//----------------------------------------------------------------------
// Constructor.
WaveformTools::WaveformTools(const fhicl::ParameterSet& pset)
{
    configure(pset);
}

void WaveformTools::configure(const fhicl::ParameterSet& pset)
{
    // Start by recovering the parameters
//    fThisPlane       = pset.get<size_t>("Plane");

    return;
}

void WaveformTools::triangleSmooth(const std::vector<double>& inputVec, std::vector<double>& smoothVec, size_t lowestBin) const
{
    triangleSmooth<double>(inputVec, smoothVec, lowestBin);

    return;
}

void WaveformTools::triangleSmooth(const std::vector<float>& inputVec, std::vector<float>& smoothVec, size_t lowestBin) const
{
    triangleSmooth<float>(inputVec, smoothVec, lowestBin);

    return;
}

template <typename T> void WaveformTools::triangleSmooth(const std::vector<T>& inputVec, std::vector<T>& smoothVec, size_t lowestBin) const
{
    if (inputVec.size() != smoothVec.size()) smoothVec.resize(inputVec.size());

    // Watch for edge condition
    if (inputVec.size() > 4)
    {
        std::copy(inputVec.begin(), inputVec.begin() + 2 + lowestBin, smoothVec.begin());
        std::copy(inputVec.end() - 2, inputVec.end(), smoothVec.end() - 2);

        typename std::vector<T>::iterator       curItr    = smoothVec.begin() + 2 + lowestBin;
        typename std::vector<T>::const_iterator curInItr  = inputVec.begin()  + 1 + lowestBin;
        typename std::vector<T>::const_iterator stopInItr = inputVec.end()    - 3;

        while(curInItr++ != stopInItr)
        {
            // Take the weighted average of five consecutive points centered on current point
            T newVal = (*(curInItr - 2) + 2. * *(curInItr - 1) + 3. * *curInItr + 2. * *(curInItr + 1) + *(curInItr + 2)) / 9.;

            *curItr++ = newVal;
        }
    }
    else std::copy(inputVec.begin(), inputVec.end(), smoothVec.begin());

    return;
}

void WaveformTools::medianSmooth(const std::vector<float>&inputVec, std::vector<float>& smoothVec, size_t nBins) const
{
    medianSmooth<float>(inputVec, smoothVec, nBins);

    return;
}

void WaveformTools::medianSmooth(const std::vector<double>& inputVec, std::vector<double>& smoothVec, size_t nBins) const
{
    medianSmooth<double>(inputVec, smoothVec, nBins);

    return;
}

template <typename T> void WaveformTools::medianSmooth(const std::vector<T>& inputVec, std::vector<T>& smoothVec, size_t nBins) const
{
    // For our purposes, nBins must be odd
    if (nBins % 2 == 0) nBins++;

    // Make sure the input vector is right sized
    if (inputVec.size() != smoothVec.size()) smoothVec.resize(inputVec.size());

    // Basic set up
    typename std::vector<T> medianVec(nBins);
    typename std::vector<T>::const_iterator startItr = inputVec.begin();
    typename std::vector<T>::const_iterator stopItr  = startItr;

    std::advance(stopItr, inputVec.size() - nBins);

    size_t medianBin = nBins/2;
    size_t smoothBin = medianBin;

    // First bins are not smoothed
    std::copy(startItr, startItr + medianBin, smoothVec.begin());

    while(std::distance(startItr,stopItr) > 0)
    {
        std::copy(startItr,startItr+nBins,medianVec.begin());
        std::sort(medianVec.begin(),medianVec.end());

        T medianVal = medianVec[medianBin];

        smoothVec[smoothBin++] = medianVal;

        startItr++;
    }

    // Last bins are not smoothed
    std::copy(startItr + medianBin, inputVec.end(), smoothVec.begin() + smoothBin);

    return;
}

void WaveformTools::getTruncatedMeanRMS(const std::vector<double>& waveform, double& mean, double& rmsFull, double& rmsTrunc, int& nTrunc) const
{
    getTruncatedMeanRMS<double>(waveform, mean, rmsFull, rmsTrunc, nTrunc);
}

void WaveformTools::getTruncatedMeanRMS(const std::vector<float>& waveform, float& mean, float& rmsFull, float& rmsTrunc, int& nTrunc) const
{
    getTruncatedMeanRMS<float>(waveform, mean, rmsFull, rmsTrunc, nTrunc);
}

template <typename T> void WaveformTools::getTruncatedMeanRMS(const std::vector<T>& waveform, T& mean, T& rmsFull, T& rmsTrunc, int& nTrunc) const
{
    // We need to get a reliable estimate of the mean and can't assume the input waveform will be ~zero mean...
    // Basic idea is to find the most probable value in the ROI presented to us
    // From that we can develop an average of the true baseline of the ROI.
    // To do that we employ a map based scheme
    std::map<int,int> frequencyMap;
    int               mpCount(0);
    int               mpVal(0);

    for(const auto& val : waveform)
    {
        int intVal = std::round(4.*val);

        frequencyMap[intVal]++;

        if (frequencyMap.at(intVal) > mpCount)
        {
            mpCount = frequencyMap.at(intVal);
            mpVal   = intVal;
        }
    }

    // take a weighted average of two neighbor bins
    int meanCnt  = 0;
    int meanSum  = 0;
    int binRange = std::min(16, int(frequencyMap.size()/2 + 1));

    for(int idx = -binRange; idx <= binRange; idx++)
    {
        std::map<int,int>::iterator neighborItr = frequencyMap.find(mpVal+idx);

        if (neighborItr != frequencyMap.end() && 5 * neighborItr->second > mpCount)
        {
            meanSum += neighborItr->first * neighborItr->second;
            meanCnt += neighborItr->second;
        }
    }

    mean = 0.25 * T(meanSum) / T(meanCnt);  // Note that bins were expanded by a factor of 4 above

    // do rms calculation - the old fashioned way and over all adc values
    typename std::vector<T> locWaveform = waveform;

    std::transform(locWaveform.begin(), locWaveform.end(), locWaveform.begin(),std::bind(std::minus<T>(),std::placeholders::_1,mean));

    // sort in ascending order so we can truncate the sume
    std::sort(locWaveform.begin(), locWaveform.end(),[](const auto& left, const auto& right){return std::fabs(left) < std::fabs(right);});

    // recalculate the rms for truncation
    rmsFull = std::inner_product(locWaveform.begin(), locWaveform.end(), locWaveform.begin(), 0.);
    rmsFull = std::sqrt(std::max(T(0.),rmsFull / T(locWaveform.size())));

    // recalculate the rms for truncation
    rmsTrunc = std::inner_product(locWaveform.begin(), locWaveform.begin() + meanCnt, locWaveform.begin(), 0.);
    rmsTrunc = std::sqrt(std::max(T(0.),rmsTrunc / T(meanCnt)));
    nTrunc   = meanCnt;

    return;
}

void WaveformTools::firstDerivative(const std::vector<double>& inputVec, std::vector<double>& derivVec) const
{
    firstDerivative<double>(inputVec, derivVec);

    return;
}

void WaveformTools::firstDerivative(const std::vector<float>& inputVec, std::vector<float>& derivVec) const
{
    firstDerivative<float>(inputVec, derivVec);

    return;
}

template <typename T> void WaveformTools::firstDerivative(const std::vector<T>& inputVec, std::vector<T>& derivVec) const
{
    derivVec.resize(inputVec.size(), 0.);

    for(size_t idx = 1; idx < derivVec.size() - 1; idx++)
        derivVec.at(idx) = 0.5 * (inputVec.at(idx + 1) - inputVec.at(idx - 1));

    return;
}

void WaveformTools::findPeaks(std::vector<double>::iterator startItr, std::vector<double>::iterator stopItr, PeakTupleVec& peakTupleVec, double threshold, size_t firstTick) const
{
    findPeaks<double>(startItr, stopItr, peakTupleVec, threshold, firstTick);

    return;
}

void WaveformTools::findPeaks(std::vector<float>::iterator startItr, std::vector<float>::iterator stopItr, PeakTupleVec& peakTupleVec, float threshold, size_t firstTick) const
{
    findPeaks<float>(startItr, stopItr, peakTupleVec, threshold, firstTick);

    return;
}

template <typename T> void WaveformTools::findPeaks(typename std::vector<T>::iterator startItr,
                                                    typename std::vector<T>::iterator stopItr,
                                                    PeakTupleVec&                     peakTupleVec,
                                                    T                                 threshold,
                                                    size_t                            firstTick) const
{
    // Need a minimum distance or else nothing to do
    if (std::distance(startItr,stopItr) > 4)
    {
        // This is a divide and conquer algorithm, start by finding the maximum element.
        typename std::vector<T>::iterator firstItr = std::max_element(startItr,stopItr,[](float left, float right){return std::fabs(left) < std::fabs(right);});

        // Are we over threshold?
        if (std::fabs(*firstItr) > threshold)
        {
            // What am I thinking?
            // First task is to find the "other" lobe max point
            // Set one to the "first", the other to the "second"
            // Search backward from first to find start point, forward from second to find end point
            // Set mid point between first and second as "peak"?
            typename std::vector<T>::iterator secondItr = firstItr;

            // Assume if max bin is positive then second lobe is later
            if (*firstItr > 0)
            {
                typename std::vector<T>::iterator tempItr = secondItr;

                while(tempItr != stopItr)
                {
                    if (*++tempItr < -threshold)
                    {
                        if (*tempItr < *secondItr) secondItr = tempItr;
                    }
                    else if (secondItr != firstItr) break;
                }
            }
            // Otherwise it goes the other way
            else
            {
                typename std::vector<T>::iterator tempItr = secondItr;

                while(tempItr != startItr)
                {
                    if (*--tempItr > threshold)
                    {
                        if (*tempItr > *secondItr) secondItr = tempItr;
                    }
                    else if (secondItr != firstItr) break;
                }

                std::swap(firstItr,secondItr);
            }

            // It might that no real pulse was found
            if (firstItr != secondItr)
            {
                // Get the "peak" position
                size_t peakBin = std::distance(startItr,firstItr) + std::distance(firstItr,secondItr) / 2;

                // Advance (forward or backward) the first and second iterators to get back to zero crossing
                while(firstItr  != startItr) if (*--firstItr  < 0.) break;
                while(secondItr != stopItr)  if (*++secondItr > 0.) break;

                size_t firstBin = std::distance(startItr,firstItr);
                size_t lastBin  = std::distance(startItr,secondItr);

                // Find leading peaks
                findPeaks(startItr, firstItr, peakTupleVec, threshold, firstTick);

                // Save this peak
                peakTupleVec.push_back(PeakTuple(firstBin+firstTick,peakBin+firstTick,lastBin+firstTick));

                // Find downstream peaks
                findPeaks(secondItr, stopItr, peakTupleVec, threshold, firstTick + std::distance(startItr,secondItr));
            }
        }
    }

    return;
}

void WaveformTools::getFFTPower(const std::vector<float>& inputVec, std::vector<float>& outputPowerVec) const
{
    std::vector<double> inputDoubleVec(inputVec.size());
    std::vector<double> outputDoubleVec(inputVec.size()/2);

    std::copy(inputVec.begin(),inputVec.end(),inputDoubleVec.begin());

    getFFTPower(inputDoubleVec, outputDoubleVec);

    if (outputDoubleVec.size() != outputPowerVec.size()) outputPowerVec.resize(outputDoubleVec.size());

    std::copy(outputDoubleVec.begin(),outputDoubleVec.end(),outputPowerVec.begin());

    return;
}

void WaveformTools::getFFTPower(const std::vector<double>& inputVec, std::vector<double>& outputPowerVec) const
{
    // Get the FFT of the response
    int fftDataSize = inputVec.size();

    TVirtualFFT* fftr2c = TVirtualFFT::FFT(1, &fftDataSize, "R2C");

    fftr2c->SetPoints(inputVec.data());
    fftr2c->Transform();

    // Recover the results so we can compute the power spectrum
    size_t halfFFTDataSize(fftDataSize/2 + 1);

    std::vector<double> realVals(halfFFTDataSize);
    std::vector<double> imaginaryVals(halfFFTDataSize);

    fftr2c->GetPointsComplex(realVals.data(), imaginaryVals.data());

    if (outputPowerVec.size() != halfFFTDataSize) outputPowerVec.resize(halfFFTDataSize,0.);

    std::transform(realVals.begin(), realVals.begin() + halfFFTDataSize, imaginaryVals.begin(), outputPowerVec.begin(), [](const double& real, const double& imaginary){return std::sqrt(real*real + imaginary*imaginary);});

    return;
}

void WaveformTools::getErosionDilationAverageDifference(const Waveform<short>& waveform,
                                                        int                    structuringElement,
                                                        HistogramMap&          histogramMap,
                                                        Waveform<short>&       erosionVec,
                                                        Waveform<short>&       dilationVec,
                                                        Waveform<short>&       averageVec,
                                                        Waveform<short>&       differenceVec)         const
{
    getErosionDilationAverageDifference<short>(waveform, structuringElement, histogramMap, erosionVec, dilationVec, averageVec, differenceVec);

    return;
}

void WaveformTools::getErosionDilationAverageDifference(const Waveform<float>& waveform,
                                                        int                    structuringElement,
                                                        HistogramMap&          histogramMap,
                                                        Waveform<float>&       erosionVec,
                                                        Waveform<float>&       dilationVec,
                                                        Waveform<float>&       averageVec,
                                                        Waveform<float>&       differenceVec)         const
{
    getErosionDilationAverageDifference<float>(waveform, structuringElement, histogramMap, erosionVec, dilationVec, averageVec, differenceVec);

    return;
}

void WaveformTools::getErosionDilationAverageDifference(const Waveform<double>& waveform,
                                                        int                     structuringElement,
                                                        HistogramMap&           histogramMap,
                                                        Waveform<double>&       erosionVec,
                                                        Waveform<double>&       dilationVec,
                                                        Waveform<double>&       averageVec,
                                                        Waveform<double>&       differenceVec)         const
{
    getErosionDilationAverageDifference<double>(waveform, structuringElement, histogramMap, erosionVec, dilationVec, averageVec, differenceVec);

    return;
}

template <typename T> void WaveformTools::getErosionDilationAverageDifference(const Waveform<T>& inputWaveform,
                                                                              int                structuringElement,
                                                                              HistogramMap&      histogramMap,
                                                                              Waveform<T>&       erosionVec,
                                                                              Waveform<T>&       dilationVec,
                                                                              Waveform<T>&       averageVec,
                                                                              Waveform<T>&       differenceVec) const
{
    // Set the window size
    int halfWindowSize(structuringElement/2);

    // Initialize min and max elements
    std::pair<typename Waveform<T>::const_iterator,typename Waveform<T>::const_iterator> minMaxItr =
            std::minmax_element(inputWaveform.begin(),inputWaveform.begin()+halfWindowSize);

    typename Waveform<T>::const_iterator minElementItr = minMaxItr.first;
    typename Waveform<T>::const_iterator maxElementItr = minMaxItr.second;

    // Initialize the erosion and dilation vectors
    erosionVec.resize(inputWaveform.size());
    dilationVec.resize(inputWaveform.size());
    averageVec.resize(inputWaveform.size());
    differenceVec.resize(inputWaveform.size());

    // Now loop through remaining elements and complete the vectors
    typename Waveform<T>::iterator minItr = erosionVec.begin();
    typename Waveform<T>::iterator maxItr = dilationVec.begin();
    typename Waveform<T>::iterator aveItr = averageVec.begin();
    typename Waveform<T>::iterator difItr = differenceVec.begin();

    for (typename Waveform<T>::const_iterator inputItr = inputWaveform.begin(); inputItr != inputWaveform.end(); inputItr++)
    {
        // There are two conditions to check:
        // 1) is the current min/max element outside the current window?
        // 2) is the new element smaller/larger than the current min/max?

        // Make sure we are not running off the end of the vector
        if (std::distance(inputItr,inputWaveform.end()) > halfWindowSize)
        {
            if (std::distance(minElementItr,inputItr) >= halfWindowSize)
                minElementItr = std::min_element(inputItr - halfWindowSize + 1, inputItr + halfWindowSize + 1);
            else if (*(inputItr + halfWindowSize) < *minElementItr)
                minElementItr = inputItr + halfWindowSize;

            if (std::distance(maxElementItr,inputItr) >= halfWindowSize)
                maxElementItr = std::max_element(inputItr - halfWindowSize + 1, inputItr + halfWindowSize + 1);
            else if (*(inputItr + halfWindowSize) > *maxElementItr)
                maxElementItr = inputItr + halfWindowSize;
        }

        // Update the vectors
        *minItr++ = *minElementItr;
        *maxItr++ = *maxElementItr;
        *aveItr++ = 0.5 * (*maxElementItr + *minElementItr);
        *difItr++ = *maxElementItr - *minElementItr;

        if (!histogramMap.empty())
        {
            int curBin = std::distance(inputWaveform.begin(),inputItr);

            histogramMap.at(WAVEFORM)->Fill(   curBin, *inputItr);
            histogramMap.at(EROSION)->Fill(    curBin, *minElementItr);
            histogramMap.at(DILATION)->Fill(   curBin, *maxElementItr);
            histogramMap.at(AVERAGE)->Fill(    curBin, 0.5*(*maxElementItr + *minElementItr));
            histogramMap.at(DIFFERENCE)->Fill( curBin,      *maxElementItr - *minElementItr);
        }

    }

    return;
}

void WaveformTools::getOpeningAndClosing(const Waveform<short>& erosionVec,
                                         const Waveform<short>& dilationVec,
                                         int                    structuringElement,
                                         HistogramMap&          histogramMap,
                                         Waveform<short>&       openingVec,
                                         Waveform<short>&       closingVec) const
{
    getOpeningAndClosing<short>(erosionVec, dilationVec, structuringElement, histogramMap, openingVec, closingVec);

    return;
}

void WaveformTools::getOpeningAndClosing(const Waveform<float>& erosionVec,
                                         const Waveform<float>& dilationVec,
                                         int                    structuringElement,
                                         HistogramMap&          histogramMap,
                                         Waveform<float>&       openingVec,
                                         Waveform<float>&       closingVec) const
{
    getOpeningAndClosing<float>(erosionVec, dilationVec, structuringElement, histogramMap, openingVec, closingVec);

    return;
}

void WaveformTools::getOpeningAndClosing(const Waveform<double>& erosionVec,
                                         const Waveform<double>& dilationVec,
                                         int                     structuringElement,
                                         HistogramMap&           histogramMap,
                                         Waveform<double>&       openingVec,
                                         Waveform<double>&       closingVec) const
{
    getOpeningAndClosing<double>(erosionVec, dilationVec, structuringElement, histogramMap, openingVec, closingVec);

    return;
}

template <typename T> void WaveformTools::getOpeningAndClosing(const Waveform<T>& erosionVec,
                                                               const Waveform<T>& dilationVec,
                                                               int                structuringElement,
                                                               HistogramMap&      histogramMap,
                                                               Waveform<T>&       openingVec,
                                                               Waveform<T>&       closingVec)  const
{
    // Set the window size
    int halfWindowSize(structuringElement/2);

    // Start with the opening, here we get the max element in the input erosion vector
    typename Waveform<T>::const_iterator maxElementItr = std::max_element(erosionVec.begin(),erosionVec.begin()+halfWindowSize);

    // Initialize the opening vector
    openingVec.resize(erosionVec.size());

    // Now loop through remaining elements and complete the vectors
    typename Waveform<T>::iterator maxItr = openingVec.begin();

    for (typename Waveform<T>::const_iterator inputItr = erosionVec.begin(); inputItr != erosionVec.end(); inputItr++)
    {
        // There are two conditions to check:
        // 1) is the current min/max element outside the current window?
        // 2) is the new element smaller/larger than the current min/max?

        // Make sure we are not running off the end of the vector
        if (std::distance(inputItr,erosionVec.end()) > halfWindowSize)
        {
            if (std::distance(maxElementItr,inputItr) >= halfWindowSize)
                maxElementItr = std::max_element(inputItr - halfWindowSize + 1, inputItr + halfWindowSize + 1);
            else if (*(inputItr + halfWindowSize) > *maxElementItr)
                maxElementItr = inputItr + halfWindowSize;
        }

        // Update the vectors
        *maxItr++ = *maxElementItr;

        if (!histogramMap.empty())
        {
            int curBin = std::distance(erosionVec.begin(),inputItr);

            histogramMap.at(OPENING)->Fill(curBin, *maxElementItr);
        }
    }

    // Now go with the closling, here we get the min element in the input dilation vector
    typename Waveform<T>::const_iterator minElementItr = std::min_element(dilationVec.begin(),dilationVec.begin()+halfWindowSize);

    // Initialize the opening and closing vectors
    closingVec.resize(dilationVec.size());

    // Now loop through remaining elements and complete the vectors
    typename Waveform<T>::iterator minItr = closingVec.begin();

    for (typename Waveform<T>::const_iterator inputItr = dilationVec.begin(); inputItr != dilationVec.end(); inputItr++)
    {
        // There are two conditions to check:
        // 1) is the current min/max element outside the current window?
        // 2) is the new element smaller/larger than the current min/max?

        // Make sure we are not running off the end of the vector
        if (std::distance(inputItr,dilationVec.end()) > halfWindowSize)
        {
            if (std::distance(minElementItr,inputItr) >= halfWindowSize)
                minElementItr = std::min_element(inputItr - halfWindowSize + 1, inputItr + halfWindowSize + 1);
            else if (*(inputItr + halfWindowSize) < *minElementItr)
                minElementItr = inputItr + halfWindowSize;
        }

        // Update the vectors
        *minItr++ = *minElementItr;

        if (!histogramMap.empty())
        {
            int curBin = std::distance(dilationVec.begin(),inputItr);

            histogramMap.at(CLOSING)->Fill(curBin, *minElementItr);
            histogramMap.at(DOPENCLOSING)->Fill(curBin, *minElementItr - openingVec.at(curBin));
        }
    }

    return;
}

DEFINE_ART_CLASS_TOOL(WaveformTools)
}