globals.h

#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<Material> MaterialList;
extern int currentMaterial;
void ChangeAbsorbance();
void SetMaterial();

//source parameters
extern vector<SpecPair> SourceSpectrum;
extern vector<SpecPair> SourceResampled;
void ResampleSource();	//resample a source profile to match the sample points of the current material
extern bool useSourceSpectrum;

//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;


//distortion maps
double ComputeDistortion();
void DistortionMap(float* distortionMap, int nSteps);


#endif