#ifndef BIOEM_H
#define BIOEM_H
#include <fstream>
#include <iostream>
#include <complex>

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

class bioem
{
public:
    bioem();
    virtual ~bioem();

    int configure(int ac, char* av[]);
    int precalculate(); // Is it better to pass directly the input File names?
    int dopreCalCrossCorrelation(int iRefMap, int iRefMapLocal);
    int run();
    int doProjections(int iMap);
    int createConvolutedProjectionMap(int iOreint,int iMap, mycomplex_t* lproj,bioem_map& Mapconv);

	virtual int compareRefMaps(int iProjectionOut, int iConv, const bioem_map& conv_map, const int startMap = 0);
    int createProjection(int iMap, mycomplex_t* map);
    int calcross_cor(bioem_map& localmap,myfloat_t& sum,myfloat_t& sumsquare);

    bioem_Probability* pProb;
	
protected:
	virtual int deviceInit();
	virtual int deviceStartRun();
	virtual int deviceFinishRun();

    bioem_param param;
    bioem_model Model;
    bioem_RefMap RefMap;

    int nReferenceMaps;			//Maps in memory at a time
    int nReferenceMapsTotal;	//Maps in total

    int nProjectionMaps;		//Maps in memory at a time
    int nProjectionMapsTotal;	//Maps in total
};

#endif