deprecated / bimsim

  #include "fileout.h"

  
  void fileoutStruct::saveNearField(nearfieldStruct* nf)
  {
      if(nearFile == "") return;
  
      if(field == fieldReal)
      {
          scalarslice S = nf->U.Real();
          S.toImage(nearFile, false, colormap);
      }
      if(field == fieldImag)
      {
          scalarslice S = nf->U.Imag();
          S.toImage(nearFile, false, colormap);
      }
      if(field == fieldMag)
      {
          scalarslice S = nf->U.Mag();
          S.toImage(nearFile, true, colormap);
      }
  }
  
  void fileoutStruct::saveFarField(microscopeStruct* scope)
  {
      if(farFile == "") return;
  
      if(field == fieldReal)
      {
          scalarslice S = scope->Ud.Real();
          S.toImage(farFile, false, colormap);
      }
      if(field == fieldImag)
      {
          scalarslice S = scope->Ud.Imag();
          S.toImage(farFile, false, colormap);
      }
      if(field == fieldMag)
      {
          scalarslice S = scope->Ud.Mag();
          S.toImage(farFile, true, colormap);
      }
  
  }
  
  void fileoutStruct::saveDetector(microscopeStruct* scope)
  {
  	//intensity
      if(intFile != "")
      {
          scalarslice I = scope->getIntensity();
  
          if(is_binary(intFile))

  		{
  			if(wavenumber)
  				I.toEnvi(intFile, 10000.0f/scope->nf.lambda, append);
  			else
  				I.toEnvi(intFile, scope->nf.lambda, append);
  		}

  		else
  			I.toImage(intFile);

      }
      //absorbance
      if(absFile != "")
      {
          scalarslice I = scope->getAbsorbance();
  
          if(is_binary(absFile))

          {
  			if(wavenumber)
  				I.toEnvi(absFile, 10000.0f/scope->nf.lambda, append);
  			else
  				I.toEnvi(absFile, scope->nf.lambda, append);
  		}

          else
              I.toImage(absFile);
      }
      //transmittance
      if(transFile != "")
      {
          scalarslice I = scope->getTransmittance();
  
          if(is_binary(transFile))

          {
  			if(wavenumber)
  				I.toEnvi(transFile, 10000.0f/scope->nf.lambda, append);
  			else
  				I.toEnvi(transFile, scope->nf.lambda, append);
  		}

          else
              I.toImage(transFile);
      }
  
  }
  
  bool fileoutStruct::is_binary(std::string filename)
  {
      //this function guesses if a file name is binary or a standard image
      //  do this by just testing extensions
  
      //get the extension
      size_t i = filename.find_last_of('.');
  
      //if there is no extension, return true
      if( i == std::string::npos )
          return true;
  
      //otherwise grab the extension
      std::string ext = filename.substr(i+1);
      if(ext == "bmp" ||
         ext == "jpg" ||
         ext == "tif" ||
         ext == "gif" ||
         ext == "png")
         return false;
      else
          return true;
  }
  
  

  

  void fileoutStruct::Save(microscopeStruct* scope)

  {
  	//save images of the fields in the microscope
  
  	//if the user specifies an extended source

  	if(scope->focalPoints.size() > 0)

  	{
  		//simulate the extended source and output the detector image
  		scope->SimulateExtendedSource();
  

  		//saveNearField(&scope->nf);
  		saveFarField(scope);
  
  		//save the detector images
  		saveDetector(scope);
  
  		//simulate scattering for the last point (so that you have a near field image)
  		scope->SimulateScattering();
          saveNearField(&scope->nf);
  

  	}
  	else
  	{
  		//run the near-field simulation
  		scope->SimulateScattering();
  
  		//output the near field image
  		saveNearField(&scope->nf);
  
  		//run the far-field simulation
  		scope->SimulateImaging();
  

  		//saveNearField(&scope->nf);

  		saveFarField(scope);
  

  		//save the detector images
  		saveDetector(scope);
  

  	}
  

  
  

  }