optics / imie

  #ifndef GLOBALS_H
  #define GLOBALS_H
  
  #include <vector>
  #include <string>
  #include <iostream>
  #include "PerformanceData.h"
  #include <complex>
  using namespace std;
  

  typedef float rtsFloat;
  

  struct SpecPair{

  	double nu;
  	double A;

  };
  
  struct Material{

  	vector<double> nu;

  	vector<complex<double> > eta;

  	string name;
  };
  
  enum SpecType {AbsorbanceSpecType, IntensitySpecType};
  enum OpticsType {TransmissionOpticsType, ReflectionOpticsType};
  
  extern PerformanceData PD;
  
  

  extern vector<vector<SpecPair> > RefSpectrum;

  extern int currentSpec;
  extern vector<SpecPair> SimSpectrum;
  
  //IO Functions
  vector<SpecPair> LoadSpectrum(string filename);
  vector<SpecPair> SetReferenceSpectrum(char* text);
  void SaveState();
  void LoadState();
  void SetDefaults();
  void SaveSimulation(string fileName);
  void SaveK(string fileName);
  void SaveN(string fileName);
  void LoadMaterial(string fileNameK, string fileNameN, string materialName);
  void LoadMaterial(string fileNameK, string materialName);
  
  //Display Functions
  void FitDisplay();
  
  //Update Functions
  void UpdateDisplay();
  void SimulateSpectrum();

  void cudaKramersKronig(double* cpuN, double* cpuK, int nVals, double nuStart, double nuEnd, double nOffset);
  void cudaComputeSpectrum(double* cpuI, double* cpuB, double* alpha,
  						 int Nl, int nLambda, double oThetaI, double oThetaO, double cThetaI, double cThetaO, int nSamples);

  
  //Window Parameters

  extern double nuMin;
  extern double nuMax;
  extern double aMin;
  extern double aMax;
  extern double dNu;

  extern bool dispRefSpec;
  extern bool dispSimSpec;
  extern bool dispSimK;
  extern bool dispMatK;
  extern bool dispSimN;
  extern bool dispMatN;
  extern SpecType dispSimType;
  extern bool dispNormalize;

  extern double dispNormFactor;

  extern double dispScaleK;
  extern double dispScaleN;

  
  //material parameters

  extern double radius;
  extern double baseIR;
  extern double cA;

  extern vector<SpecPair> EtaK;
  extern vector<SpecPair> EtaN;
  extern bool applyMaterial;
  //extern vector<SpecPair> KMaterial;
  //extern vector<SpecPair> NMaterial;
  extern vector<Material> MaterialList;
  extern int currentMaterial;
  void ChangeAbsorbance();
  void SetMaterial();
  
  //optical parameters

  extern double cNAi;
  extern double cNAo;
  extern double oNAi;
  extern double oNAo;

  extern OpticsType opticsMode;
  extern bool pointDetector;
  extern int objectiveSamples;
  
  //fitting parameters

  extern double minMSE;

  extern int maxFitIter;
  void EstimateMaterial();

  extern double scaleI0;
  extern double refSlope;

  double ComputeDistortion();

  void MinimizeDistortion();
  
  
  #endif