EstimateMaterial.cpp 3.16 KB
#include "globals.h"
#include <stdlib.h>
#define PI 3.14159

double CalculateError(double* E)
    //Calculate the error between the Reference Spectrum and the Simulated Spectrum
    double sumE = 0.0;
    int nVals = RefSpectrum[currentSpec].size();
    double nu;
    for(int i=0; i<nVals; i++)
        nu = RefSpectrum[currentSpec][i].nu;
        E[i] = RefSpectrum[currentSpec][i].A + nu * refSlope - SimSpectrum[i].A;
        sumE += E[i]*E[i];

    return sumE/nVals;

void EstimateK(double* E)
    int nVals = RefSpectrum[currentSpec].size();
    double nuStart = RefSpectrum[currentSpec].front().nu;
    double nuEnd = RefSpectrum[currentSpec].back().nu;

    double r = radius/10000.0;
    double nu;
    double dNu = (nuEnd - nuStart)/(nVals-1);
    double eScale;
    for(int i=0; i<nVals; i++)
        nu = nuStart + i*2;

        eScale = 1/(8*PI*r*nu);
        EtaK[i].A = EtaK[i].A + eScale * E[i];
        if(EtaK[i].A < 0.0) EtaK[i].A = 0.0;

void EstimateMaterial()
    /*This function estimates the material properties of a sphere based on the
    input spectrum RefSpectrum and the optical properties of the system.
    1) The material properties are stored in EtaK and EtaN
    2) The best fit is stored in SimSpectrum*/

    //initialize the material index of refraction

    //insert the default material properties
    SpecPair temp;
    for(int s=0; s<(int)RefSpectrum[currentSpec].size(); s++)
        //the real part of the IR is the user-specified baseline IR = RefSpectrum[currentSpec][s].nu;
        temp.A = baseIR;
        //the imaginary part of the IR is zero absorbance
        temp.A = 0.0f;

    //allocate space to store the list of error values
    double* E = (double*)malloc(sizeof(double) * RefSpectrum[currentSpec].size());
    //copy the absorbance values into a linear array
    double* k = (double*)malloc(sizeof(double) * EtaK.size());
    double* n = (double*)malloc(sizeof(double) * EtaN.size());

    //iterate to solve for both n and k
    double sumE = 99999.9;
    int j=0;
    //clear the console
    while(sumE > minMSE && j < maxFitIter)
        //simulate a spectrum based on the current IR

        //calculate the error term
        sumE = CalculateError(E);

        //estimate the new absorbance

        //use Kramers-Kronig to compute n

        for(unsigned int i=0; i<EtaK.size(); i++)
            k[i] = EtaK[i].A;
        cudaKramersKronig(n, k, EtaK.size(), EtaK.front().nu, EtaK.back().nu, baseIR);

        //copy the real part of the index of refraction into the vector
        for(int i=0; i<(int)EtaK.size(); i++)
   =  EtaK[i].nu;
            temp.A = n[i];

        cout<<"    E = "<<sumE<<endl;
        //SaveSpectrum(n, nVals, "simNj.txt");
        //SaveSpectrum(k, nVals, "simKj.txt");
        //SaveSpectrum(simSpec, nVals, "simSpec.txt");