correlationhist.cpp

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/* correlationhist.cpp : Sample program to create a cross-correlation histogram
 * 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/>.
 */

//This example creates an ion cross-correlation histogram
// as described by Saxey et al.
// DOI : 10.1016/j.ultramic.2010.11.021


#include <iostream>

#include "atomprobe/atomprobe.h"

using namespace std;
using namespace AtomProbe;


void dumpHistogram(std::vector<std::vector< unsigned int> > &hist, float step)
{

    //write the mass headings
    for(unsigned int ui=0;ui<hist.size();ui++)
    {
        cout << step*ui << "\t";

        for(unsigned int uj=0;uj<hist.size();uj++)
        {
            cout << hist[ui][uj] << "\t";
        }       

        cout << endl;
    }
}

int main(int argc, char *argv[]) 
{
    //Check for correct program usage
    if(argc != 3)
    {
        //print error message, and exit
        cerr << "USAGE : " << argv[0] << " EPOSFILE MASS_STEP" << endl;
        return 1;
    }

    //Get the user-specified histogram step size
    float stepSize;
    if(stream_cast(stepSize,argv[2]))
    {
        cerr << "Unable to understand stepsize :" << argv[2] << endl;
        return 1;
    }

    if(stepSize <=0)
    {
        cerr << "Stepsize must be nonzero and positive " << endl;
        return 2;
    }

    //Load the file 
    std::string filename = argv[1];
    cerr << "Processing file :" << filename << endl;

    vector<vector<unsigned int> > histogram;
    unsigned int offset=0;
    unsigned int entriesLeft;
    const float END_MASS=300;

    ProgressBar pb;
    pb.setLength(50);
    pb.init();

    while(true)
    {

        const unsigned int CHUNK_SIZE=1e4;
        vector<EPOS_ENTRY> eposIons;
        unsigned int errCode;
        if((errCode=chunkLoadEposFile(eposIons,filename.c_str(),CHUNK_SIZE,
            offset,entriesLeft)))
        {
            pb.finish();
            cerr << "Unable to load file :" << filename << endl;
            cerr << " reason :" << errCode << endl;
            return 2;
        }

        offset++;

        //Update progress
        pb.update(100.0f*(float)offset/(float)(offset+entriesLeft/CHUNK_SIZE));

        if(!entriesLeft)
            break;


        if(!accumulateCorrelationHistogram
            (eposIons,histogram,stepSize,END_MASS))
        {
            cerr << "Correlation histogram generation failed. Are ions sequenced correctly??" << endl;
            return 2;
            
        }
    }




    dumpHistogram(histogram,stepSize);

}