bioem.cpp 21.6 KB
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#include <fstream>
#include <boost/program_options.hpp>
#include <iostream>
#include <algorithm>
#include <iterator>
#include <stdio.h>
#include <stdlib.h>
#include <string>
#include <cmath>
#include <omp.h>

#include <fftw3.h>
#include <math.h>
#include "cmodules/timer.h"

#include "param.h"
#include "bioem.h"
#include "model.h"
#include "map.h"


#include "bioem_algorithm.h"


using namespace boost;
namespace po = boost::program_options;

using namespace std;

// A helper function of Boost
template<class T>
ostream& operator<<(ostream& os, const vector<T>& v)
{
    copy(v.begin(), v.end(), ostream_iterator<T>(os, " "));
    return os;
}

bioem::bioem()
{
	
}

bioem::~bioem()
{
	
}

int bioem::configure(int ac, char* av[])
{
    /**************************************************************************************/
    /**** Configuration Routine using boost for extracting parameters, models and maps ****/
    /**************************************************************************************/
    /****** And Precalculating necessary grids, map crosscorrelations and kernels  ********/
    /*************************************************************************************/

    /*** Inizialzing default variables ***/
    std::string infile,modelfile,mapfile;
    Model.readPDB=false;
    param.writeAngles=false;
	RefMap.dumpMap = false;
	RefMap.loadMap = false;

    /*************************************************************************************/
    cout << " ++++++++++++ FROM COMMAND LINE +++++++++++\n\n";
    /*************************************************************************************/

    /********************* Command line reading input with BOOST ************************/

    try {
        po::options_description desc("Command line inputs");
        desc.add_options()
        ("Inputfile", po::value<std::string>(), "Name of input parameter file")
        ("Modelfile", po::value< std::string>() , "Name of model file")
        ("Particlesfile", po::value< std::string>(), "Name of paricles file")
        ("ReadPDB", "(Optional) If reading model file in PDB format")
		("DumpMaps", "(Optional) Dump maps after they were red from maps file")
		("LoadMapDump", "(Optional) Read Maps from dump instead of maps file")
        ("help", "(Optional) Produce help message")
        ;

        po::positional_options_description p;
        p.add("Inputfile", -1);
        p.add("Modelfile", -1);
        p.add("Particlesfile", -1);
        p.add("ReadPDB", -1);
		p.add("DumpMaps", -1);
		p.add("LoadMapDump", -1);

        po::variables_map vm;
        po::store(po::command_line_parser(ac, av).
                  options(desc).positional(p).run(), vm);
        po::notify(vm);

        if((ac < 6)) {
            std::cout << desc << std::endl;
            return 0;
        }
        if (vm.count("help")) {
            cout << "Usage: options_description [options]\n";
            cout << desc;
            return 0;
        }

        if (vm.count("Inputfile"))
        {
            cout << "Input file is: ";
            cout << vm["Inputfile"].as< std::string >()<< "\n";
            infile=vm["Inputfile"].as< std::string >();
        }
        if (vm.count("Modelfile"))
        {
            cout << "Model file is: "
                 << vm["Modelfile"].as<  std::string  >() << "\n";
            modelfile=vm["Modelfile"].as<  std::string  >();
        }

        if (vm.count("ReadPDB"))
        {
            cout << "Reading model file in PDB format.\n";
            Model.readPDB=true;
        }
        
        if (vm.count("DumpMaps"))
        {
            cout << "Dumping Maps after reading from file.\n";
            RefMap.dumpMap = true;
        }
        
        if (vm.count("LoadMapDump"))
        {
            cout << "Loading Map dump.\n";
            RefMap.loadMap = true;
        }        

        if (vm.count("Particlesfile"))
        {
            cout << "Paricle file is: "
                 << vm["Particlesfile"].as< std::string >() << "\n";
            mapfile=vm["Particlesfile"].as< std::string >();
        }
    }
    catch(std::exception& e)
    {
        cout << e.what() << "\n";
        return 1;
    }

    /********************* Reading Parameter Input ***************************/
    // copying inputfile to param class
    param.fileinput = infile.c_str();
    param.readParameters();

    /********************* Reading Model Input ******************************/
    // copying modelfile to model class
    Model.filemodel = modelfile.c_str();
    Model.readModel();

    /********************* Reading Particle Maps Input **********************/
    /********* HERE: PROBLEM if maps dont fit on the memory!! ***************/
    // copying mapfile to ref map class
    RefMap.filemap = mapfile.c_str();
    RefMap.readRefMaps();

    /****************** Precalculating Necessary Stuff *********************/
    precalculate();
	
	param.nTotGridAngles = 10;
	param.nTotCTFs = 10;
	//param.param_device.maxDisplaceCenter = 0;
	
	deviceInit();

    return(0);
}

int bioem::precalculate()
{
    /**************************************************************************************/
    /* Precalculating Routine of Orientation grids, Map crosscorrelations and CTF Kernels */
    /**************************************************************************************/

    // Generating Grids of orientations
    param.CalculateGridsParam();

    //Inizialzing crosscorrelations of Maps
    memset(RefMap.sum_RefMap, 0, BIOEM_MAX_MAPS * sizeof(*RefMap.sum_RefMap));
    memset(RefMap.sumsquare_RefMap, 0, BIOEM_MAX_MAPS * sizeof(*RefMap.sum_RefMap));

    myfloat_t sum,sumsquare;

    //Precalculating cross-correlations of maps
    for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap ; iRefMap++)
    {
        calcross_cor(RefMap.Ref[iRefMap],sum,sumsquare);
        //Storing Crosscorrelations in Map class
        RefMap.sum_RefMap[iRefMap]=sum;
        RefMap.sumsquare_RefMap[iRefMap]=sumsquare;
    }

    // Precalculating CTF Kernels stored in class Param
    param.CalculateRefCTF();

    return(0);
}


int bioem::run()
{
    /**************************************************************************************/
    /**** Main BioEM routine, projects, convolutes and compares with Map using OpenMP ****/
    /**************************************************************************************/

    /**** If we want to control the number of threads -> omp_set_num_threads(XX); ******/
    /****************** Declarying class of Probability Pointer  *************************/
    pProb = new bioem_Probability[RefMap.ntotRefMap];

    printf("\tInitializing\n");
    // Inizialzing Probabilites to zero and constant to -Infinity
    for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
    {
        pProb[iRefMap].Total=0.0;
        pProb[iRefMap].Constoadd=-9999999;
        pProb[iRefMap].max_prob=-9999999;
        for (int iOrient = 0; iOrient < param.nTotGridAngles; iOrient ++)
		{
            pProb[iRefMap].forAngles[iOrient]=0.0;
            pProb[iRefMap].ConstAngle[iOrient]=-99999999;
        }
    }
    /**************************************************************************************/
	deviceStartRun();

    /******************************** MAIN CYCLE ******************************************/
	
    /*** Declaring Private variables for each thread *****/
    mycomplex_t* proj_mapFFT;
    bioem_map conv_map;

	//allocating fftw_complex vector
    proj_mapFFT= (mycomplex_t *) fftw_malloc(sizeof(mycomplex_t) *4*param.param_device.NumberPixels*param.param_device.NumberPixels);

	HighResTimer timer;

	printf("\tMain Loop (GridAngles %d, CTFs %d, RefMaps %d, Shifts (%d/%d)²), Pixels %d²\n", param.nTotGridAngles, param.nTotCTFs, RefMap.ntotRefMap, 2 * param.param_device.maxDisplaceCenter + param.param_device.GridSpaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels);
	printf("\tInner Loop Count (%d %d %d) %lld\n", param.param_device.maxDisplaceCenter, param.param_device.GridSpaceCenter, param.param_device.NumberPixels, (long long int) (param.param_device.NumberPixels * param.param_device.NumberPixels * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1) * (2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1)));
    //#pragma omp parallel for
    for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
    {
        /***************************************************************************************/
        /***** Creating Projection for given orientation and transforming to Fourier space *****/
		timer.ResetStart();
        createProjection(iProjectionOut, proj_mapFFT);
		printf("Time Projection %d: %f\n", iProjectionOut, timer.GetCurrentElapsedTime());

        /***************************************************************************************/
        /***** **** Internal Loop over convolutions **** *****/
        for (int iConv = 0; iConv < param.nTotCTFs; iConv++)
        {
			printf("\t\tConvolution %d %d\n", iProjectionOut, iConv);
            /*** Calculating convolutions of projection map and crosscorrelations ***/
			timer.ResetStart();
            createConvolutedProjectionMap(iProjectionOut,iConv,proj_mapFFT,conv_map);
			printf("Time Convolution %d %d: %f\n", iProjectionOut, iConv, timer.GetCurrentElapsedTime());

            /***************************************************************************************/
            /*** Comparing each calculated convoluted map with all experimental maps ***/
			timer.ResetStart();
			compareRefMaps(iProjectionOut, iConv, conv_map);
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			const double compTime = timer.GetCurrentElapsedTime();
			const int nShifts = 2 * param.param_device.maxDisplaceCenter / param.param_device.GridSpaceCenter + 1;
			const double nFlops = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
				(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 5. + 25.) / compTime;
			const double nGBs = (double) RefMap.ntotRefMap * (double) nShifts * (double) nShifts *
				(((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * ((double) param.param_device.NumberPixels - (double) param.param_device.maxDisplaceCenter / 2.) * 2. + 8.) * (double) sizeof(myfloat_t) / compTime;
			const double nGBs2 = (double) RefMap.ntotRefMap * ((double) param.param_device.NumberPixels * (double) param.param_device.NumberPixels + 8.) * (double) sizeof(myfloat_t) / compTime;

			printf("Time Comparison %d %d: %f sec (%f GFlops, %f GB/s (cached), %f GB/s)\n", iProjectionOut, iConv, compTime, nFlops / 1000000000., nGBs / 1000000000., nGBs2 / 1000000000.);
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        }

    }
    //deallocating fftw_complex vector
    fftw_free(proj_mapFFT);
	
	deviceFinishRun();

    /************* Writing Out Probabilities ***************/

    /*** Angular Probability ***/

    // if(param.writeAngles){
    ofstream angProbfile;
    angProbfile.open ("ANG_PROB_iRefMap");
    // }

    ofstream outputProbFile;
    outputProbFile.open ("Output_Probabilities");

    for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
    {
        /**** Total Probability ***/
        outputProbFile << "RefMap " << iRefMap << " Probability  "  << log(pProb[iRefMap].Total)+pProb[iRefMap].Constoadd+0.5*log(M_PI)+(1-param.param_device.Ntotpi*0.5)*(log(2*M_PI)+1)+log(param.param_device.volu) << " Constant " << pProb[iRefMap].Constoadd  << "\n";

        outputProbFile << "RefMap " << iRefMap << " Maximizing Param: ";

        /*** Param that maximize probability****/
        outputProbFile << (pProb[iRefMap].max_prob + 0.5 * log(M_PI) + (1 - param.param_device.Ntotpi * 0.5) * (log(2 * M_PI) + 1) + log(param.param_device.volu)) << " ";
        outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[0] << " ";
        outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[1] << " ";
        outputProbFile << param.angles[pProb[iRefMap].max_prob_orient].pos[2] << " ";
        outputProbFile << param.CtfParam[pProb[iRefMap].max_prob_conv].pos[0] << " ";
        outputProbFile << param.CtfParam[pProb[iRefMap].max_prob_conv].pos[1] << " ";
        outputProbFile << param.CtfParam[pProb[iRefMap].max_prob_conv].pos[2] << " ";
		outputProbFile << pProb[iRefMap].max_prob_cent_x << " ";
		outputProbFile << pProb[iRefMap].max_prob_cent_y;
        outputProbFile << "\n";

        /*** For individual files***/ //angProbfile.open ("ANG_PROB_"iRefMap);

        if(param.writeAngles)
		{
            for (int iProjectionOut = 0; iProjectionOut < param.nTotGridAngles; iProjectionOut++)
            {
                angProbfile << " " << iRefMap << " " << param.angles[iProjectionOut].pos[0] << " " << param.angles[iProjectionOut].pos[1] << " " << param.angles[iProjectionOut].pos[2] << " " << log(pProb[iRefMap].forAngles[iProjectionOut])+pProb[iRefMap].ConstAngle[iProjectionOut]+0.5*log(M_PI)+(1-param.param_device.Ntotpi*0.5)*(log(2*M_PI)+1)+log(param.param_device.volu) << " " << log(param.param_device.volu) << "\n";

            }
        }

    }

    angProbfile.close();
    outputProbFile.close();

    //Deleting allocated pointers

    if (pProb)
    {
        delete[] pProb;
        pProb = NULL;
    }

    if (param.refCTF)
    {
        delete[] param.refCTF;
        param.refCTF =NULL;
    }

    return(0);
}

int bioem::compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map)
{
#pragma omp parallel for
    for (int iRefMap = 0; iRefMap < RefMap.ntotRefMap; iRefMap ++)
    {
        compareRefMapShifted<-1>(iRefMap,iProjectionOut,iConv,conv_map, pProb, param.param_device, RefMap);
    }
    return(0);
}

int bioem::createProjection(int iMap,mycomplex_t* mapFFT)
{

    /**************************************************************************************/
    /****  BioEM Create Projection routine in Euler angle predefined grid****************
     ********************* and turns projection into Fourier space **********************/
    /**************************************************************************************/

    myfloat3_t RotatedPointsModel[Model.nPointsModel];
    myfloat_t rotmat[3][3];
    myfloat_t alpha, gam,beta;
    fftw_plan plan;
    mycomplex_t* localproj;
    int totnumPixFFT=2*param.param_device.NumberPixels;

    localproj= (mycomplex_t *) fftw_malloc(sizeof(mycomplex_t) *4*param.param_device.NumberPixels*param.param_device.NumberPixels);
    memset(localproj,0,4*param.param_device.NumberPixels*param.param_device.NumberPixels*sizeof(*localproj));

    alpha=param.angles[iMap].pos[0];
    beta=param.angles[iMap].pos[1];
    gam=param.angles[iMap].pos[2];

    /**** To see how things are going: cout << "Id " << omp_get_thread_num() <<  " Angs: " << alpha << " " << beta << " " << gam << "\n"; ***/

    /********** Creat Rotation with pre-defiend grid of orientations**********/

    rotmat[0][0]=cos(gam)*cos(alpha)-cos(beta)*sin(alpha)*sin(gam);
    rotmat[0][1]=cos(gam)*sin(alpha)+cos(beta)*cos(alpha)*sin(gam);
    rotmat[0][2]=sin(gam)*sin(beta);
    rotmat[1][0]=-sin(gam)*cos(alpha)-cos(beta)*sin(alpha)*cos(gam);
    rotmat[1][1]=-sin(gam)*sin(alpha)+cos(beta)*cos(alpha)*cos(gam);
    rotmat[1][2]=cos(gam)*sin(beta);
    rotmat[2][0]=sin(beta)*sin(alpha);
    rotmat[2][1]=-sin(beta)*cos(alpha);
    rotmat[2][2]=cos(beta);


    for(int n=0; n< Model.nPointsModel; n++)
	{
        RotatedPointsModel[n].pos[0]=0.0;
        RotatedPointsModel[n].pos[1]=0.0;
        RotatedPointsModel[n].pos[2]=0.0;
    }
    for(int n=0; n< Model.nPointsModel; n++)
    {
        for(int k=0; k< 3; k++)
        {
            for(int j=0; j< 3; j++)
            {
                RotatedPointsModel[n].pos[k]+=rotmat[k][j]*Model.PointsModel[n].pos[j];
            }
        }
    }

    int i, j;

    /************ Projection over the Z axis********************/
    for(int n=0; n< Model.nPointsModel; n++)
    {
        //Getting pixel that represents coordinates & shifting the start at to Numpix/2,Numpix/2 )
        i=floor(RotatedPointsModel[n].pos[0]/(*param.pixelSize)+float(param.param_device.NumberPixels)/2.0+0.5);
        j=floor(RotatedPointsModel[n].pos[1]/(*param.pixelSize)+float(param.param_device.NumberPixels)/2.0+0.5);

        localproj[i*2*param.param_device.NumberPixels+j+param.param_device.NumberPixels*param.param_device.NumberPixels+int(param.param_device.NumberPixels/2.0)][0]+=Model.densityPointsModel[n];

    }

    /**** Output Just to check****/
    if(iMap==10)
    {
        ofstream myexamplemap;
        ofstream myexampleRot;
        myexamplemap.open ("MAP_i10");
        myexampleRot.open ("Rot_i10");
        myexamplemap << "ANGLES " << alpha << " " << beta << " " << gam << "\n";
        for(int k=0; k<2*param.param_device.NumberPixels; k++)
        {
            for(int j=0; j<2*param.param_device.NumberPixels; j++) myexamplemap << "\nMAP " << k << " " << j<< " " <<localproj[k*2*param.param_device.NumberPixels+j][0];
        }
        myexamplemap << " \n";
        for(int n=0; n< Model.nPointsModel; n++)myexampleRot << "\nCOOR " << RotatedPointsModel[n].pos[0] << " " << RotatedPointsModel[n].pos[1] << " " << RotatedPointsModel[n].pos[2];
        myexamplemap.close();
        myexampleRot.close();
    }

    /***** Converting projection to Fourier Space for Convolution later with kernel****/
    /********** Omp Critical is necessary with FFTW*******/
    //#pragma omp critical
    {
        plan = fftw_plan_dft_2d(totnumPixFFT,totnumPixFFT,localproj,mapFFT,FFTW_FORWARD,FFTW_ESTIMATE);
        fftw_execute(plan);
        fftw_destroy_plan(plan);
        fftw_free(localproj);
    }

    return(0);
}


int bioem::createConvolutedProjectionMap(int iMap,int iConv,mycomplex_t* lproj,bioem_map& Mapconv)
{
    /**************************************************************************************/
    /****  BioEM Create Convoluted Projection Map routine, multiplies in Fourier **********
    **************** calculated Projection with convoluted precalculated Kernel**********
    *************** and Backtransforming it to real Space ******************************/
    /**************************************************************************************/

    fftw_plan plan;
    mycomplex_t* localmultFFT;
    mycomplex_t* localconvFFT;
    int totnumPixFFT=2*param.param_device.NumberPixels;
    localmultFFT= (mycomplex_t *) fftw_malloc(sizeof(mycomplex_t)*totnumPixFFT*totnumPixFFT);
    localconvFFT= (mycomplex_t *) fftw_malloc(sizeof(mycomplex_t)*totnumPixFFT*totnumPixFFT);


    /**** Multiplying FFTmap with corresponding kernel ****/

    for(int i=0; i < 2*param.param_device.NumberPixels ; i++ )
    {
        for(int j=0; j < 2*param.param_device.NumberPixels ; j++ )
        {   //Projection*CONJ(KERNEL)
            localmultFFT[i*2*param.param_device.NumberPixels+j][0]=lproj[i*2*param.param_device.NumberPixels+j][0]*param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][0]+lproj[i*2*param.param_device.NumberPixels+j][1]*param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][1];
            localmultFFT[i*2*param.param_device.NumberPixels+j][1]=lproj[i*2*param.param_device.NumberPixels+j][1]*param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][0]-lproj[i*2*param.param_device.NumberPixels+j][0]*param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][1];
            // cout << "GG " << i << " " << j << " " << param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][0] << " " <<param.refCTF[iConv].cpoints[i*2*param.param_device.NumberPixels+j][1] <<" " <<lproj[i*2*param.param_device.NumberPixels+j][0] <<" " <<lproj[i*2*param.param_device.NumberPixels+j][1] << "\n";
        }
    }

    /**** Bringing convoluted Map to real Space ****/
    //#pragma omp critical
    {
        plan = fftw_plan_dft_2d(totnumPixFFT,totnumPixFFT,localmultFFT,localconvFFT,FFTW_BACKWARD,FFTW_ESTIMATE);
        fftw_execute(plan);
    }


    /****Asigning convolution fftw_complex to bioem_map ****/
    for(int i=0; i < param.param_device.NumberPixels ; i++ )
    {
        for(int j=0; j < param.param_device.NumberPixels ; j++ )
        {
            Mapconv.points[i][j]=localconvFFT[i*2*param.param_device.NumberPixels+j+param.param_device.NumberPixels*param.param_device.NumberPixels+int(param.param_device.NumberPixels/2.0)][0];
        }
    }

    /**** Freeing fftw_complex created (dont know if omp critical is necessary) ****/
    //#pragma omp critical
    {
        fftw_destroy_plan(plan);
        fftw_free(localconvFFT);
        fftw_free(localmultFFT);
    }

    return(0);
}

int bioem::calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare)
{
    /*********************** Routine to calculate Cross correlations***********************/

    sum=0.0;
    sumsquare=0.0;
    for (int i = 0; i < param.param_device.NumberPixels; i++)
    {
        for (int j = 0; j < param.param_device.NumberPixels; j++)
        {
            // Calculate Sum of pixels
            sum += localmap.points[i][j];
            // Calculate Sum of pixels squared
            sumsquare += localmap.points[i][j]*localmap.points[i][j];
        }
    }
    return(0);
}

int bioem::deviceInit()
{
	return(0);
}

int bioem::deviceStartRun()
{
	return(0);
}

int bioem::deviceFinishRun()
{
	return(0);
}