histogram.cpp

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/* 
* histogram.cpp - Precise KD tree implementation
* Copyright (C) 2015  Daniel Haley
* 
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* 
* This program 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 General Public License for more details.
* 
* You should have received a copy of the GNU General Public License
* along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/
#include "atomprobe/algorithm/histogram.h"

#include "atomprobe/helper/aptAssert.h"
#include <limits>

using std::vector;

namespace AtomProbe
{


bool incrementCorrelationHist(const std::vector<EPOS_ENTRY> &eposIons,
        std::vector<std::vector<unsigned int> > &histogram,float stepMass,
        float endMass)
{
    #pragma omp parallel for
    for(unsigned int ui=0; ui<eposIons.size();ui++) 
    {
        unsigned int nMultihits;
        nMultihits =eposIons[ui].hitMultiplicity;

        //zero implies not the start of a multihit sequence
        // 1 implies only a single hit
        if(nMultihits  <= 1)
            continue;

        //loop over every possible combination of multi-hit pairings
        // but only the lower-triangular section
        for(unsigned int uj=0;uj<nMultihits; uj++)
        {
            for(unsigned int uk=uj+1;uk<nMultihits; uk++)
            {
                //find the masses of the two hits
                float m1,m2;
                m1 =eposIons[ui+uj].massToCharge;
                m2 =eposIons[ui+uk].massToCharge;
                unsigned int x,y;
                x=m1/stepMass;
                y=m2/stepMass;

                if(x >=histogram.size() || y>=histogram.size())
                    continue;

                //Data is not always ordered
                if(x > y)
                    std::swap(x,y);
                //increment the histogram.
                // break into two steps to minimise 
                // thread locking time (maybe.)
                unsigned int *v;
                v = &(histogram[x][y]);

                #pragma atomic
                (*v)++;
            }   

        }

        ui+=nMultihits;

    }



}
    

bool correlationHistogram(const std::vector<EPOS_ENTRY> &eposIons,
        std::vector<std::vector<unsigned int> > &histogram,float stepMass,
        float endMass, bool lowerTriangular)
{

    if(stepMass < sqrt(std::numeric_limits<float>::epsilon())
        || endMass < sqrt(std::numeric_limits<float>::epsilon()) )
        return false;

    const unsigned int nBins = endMass/stepMass;
    histogram.clear();
    histogram.resize(nBins);
    for(unsigned int ui=0;ui<nBins;ui++)
        histogram[ui].resize(nBins,0);

    incrementCorrelationHist(eposIons,histogram,stepMass,endMass);

    if(!lowerTriangular)
    {
        //Loop over the upper-trianglular part of the array
        for(unsigned int ui=0;ui<nBins;ui++)
        {
            for(unsigned int uj=ui+1;uj<nBins;uj++)
            {
                //mirror the histogram, copying from lower-triangular
                // component
                histogram[uj][ui]=histogram[ui][uj];
            }
        }
    }

    return true;
}

bool accumulateCorrelationHistogram(const std::vector<EPOS_ENTRY> &eposIons,
        std::vector<std::vector<unsigned int> > &histogram,float stepMass,
        float endMass, bool lowerTriangular)
{

    if(stepMass < sqrt(std::numeric_limits<float>::epsilon()) 
        || endMass < sqrt(std::numeric_limits<float>::epsilon()) )
        return false;
    
    const unsigned int nBins = endMass/stepMass;
    if(!histogram.size())
    {
        histogram.resize(nBins);

        for(unsigned int ui=0;ui<nBins;ui++)
            histogram[ui].resize(nBins,0);
    }

    incrementCorrelationHist(eposIons,histogram,stepMass,endMass);

    if(!lowerTriangular)
    {
        //Loop over the upper-trianglular part of the array
        for(unsigned int ui=0;ui<nBins;ui++)
        {
            for(unsigned int uj=ui+1;uj<nBins;uj++)
            {
                //mirror the histogram, copying from lower-triangular
                // component
                histogram[uj][ui]=histogram[ui][uj];
            }
        }
    }


    return true;
}


}