deprecated / bimsim

  #include "sphere.h"

  #include "rts/optics/material.h"

  #include <vector>
  //#include "rts/complex.h"
  
  #include "nearfield.h"
  //nearfieldStruct* NF;
  
  #include "microscope.h"
  microscopeStruct* SCOPE;
  
  #include "fieldslice.h"
  
  #include "fileout.h"
  #include "options.h"
  #include "montecarlo.h"

  #include "rts/math/point.h"
  #include "rts/math/spherical_bessel.h"
  #include "rts/math/matrix.h"
  #include "rts/math/quaternion.h"

  #include "rts/envi/envi.h"

  
  #include "warnings.h"
  
  fileoutStruct gFileOut;
  using namespace std;
  
  int cbessjyva(double v,complex<double> z,double &vm,complex<double>*cjv,

      complex<double>*cyv,complex<double>*cjvp,complex<double>*cyvp);
  
  int main(int argc, char *argv[])
  {
  	//test Envi loading and saving
  	//EnviFile envi("testenvi", "w");
  
  	//float* data = (float*)malloc(sizeof(float) * 100 * 100);
  	//envi.addBand(data, 100, 100, 100);
  
  	//envi.close();
  
  	//return 0;
  
  	SCOPE = new microscopeStruct();
  
      cout<<SCOPE->nf.Uf.R[0]<<endl;
  
      LoadParameters(argc, argv);
  
      //TestSimulation(NF, SCOPE, &gFileOut);
  
  	//initialize GPU memory for fields
  	SCOPE->init();
  
      OutputOptions();
  
  	gFileOut.Save(SCOPE);
  
  	//NF->destroy();
  	SCOPE->destroy();
  
  

  
  }