main.cpp
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#include <fstream>
#include <iostream>
using namespace std;
#include "interactivemie.h"
#include <QtGui/QApplication>
#include <QGraphicsScene>
#include <QGraphicsView>
#include <QGraphicsPixmapItem>
#include <QLayout>
#include "qtSpectrumDisplay.h"
#include "globals.h"
#include "rtsGUIConsole.h"
#include "PerformanceData.h"
#include <complex>
//#include <direct.h>
PerformanceData PD;
qtSpectrumDisplay* gpSpectrumDisplay;
QGraphicsScene* distortionScene = NULL;
QGraphicsView* distortionWindow = NULL;
QGraphicsPixmapItem* pixmapItem = NULL;
vector<vector<SpecPair> > RefSpectrum;
vector<SpecPair> SimSpectrum;
vector<SpecPair> EtaK;
vector<SpecPair> EtaN;
//source spectrum
bool useSourceSpectrum = false;
vector<SpecPair> SourceSpectrum;
//resample the source based on the material samples (EtaK and EtaN)
vector<SpecPair> SourceResampled;
int currentSpec = 0;
double nuMin = 800;
double nuMax = 4000;
double dNu = 2;
double aMin = 0;
double aMax = 1;
double scaleI0 = 1.0;
double refSlope = 0.0;
bool dispRefSpec = true;
bool dispSimSpec = true;
bool dispSimK = true;
bool dispMatK = true;
bool dispSimN = true;
bool dispMatN = true;
double dispScaleK = 1.0;
double dispScaleN = 1.0;
SpecType dispSimType = AbsorbanceSpecType;
bool dispNormalize = false;
double dispNormFactor = 1.0;
//material parameters
double radius = 4.0f;
double baseIR = 1.49f;
double cA = 1.0;
//vector<SpecPair> KMaterial;
//vector<SpecPair> NMaterial;
bool applyMaterial = true;
vector<Material> MaterialList;
int currentMaterial = 0;
//optical parameters
double cNAi = 0.0;
double cNAo = 0.6;
double oNAi = 0.0;
double oNAo = 0.6;
OpticsType opticsMode = TransmissionOpticsType;
bool pointDetector = false;
int objectiveSamples = 200;
//fitting parameters
double minMSE = 0.00001;
int maxFitIter = 20;
void TempSimSpectrum()
{
SpecPair temp;
for(int i=800; i<4000; i++)
{
temp.nu = i;
temp.A = sin((double)i/200);
SimSpectrum.push_back(temp);
}
}
void UpdateDisplay(){
gpSpectrumDisplay->updateGL();
}
void LoadMaterial(string fileNameK, string fileNameN, string materialName)
{
Material newMaterial;
newMaterial.name = materialName;
vector<SpecPair> KMaterial = LoadSpectrum(fileNameK.c_str());
vector<SpecPair> NMaterial = LoadSpectrum(fileNameN.c_str());
//make sure that the sizes are the same
if(KMaterial.size() != NMaterial.size()){
cout<<"Error, material properties don't match."<<endl;
exit(1);
}
complex<double> eta;
//int j;
for(unsigned int i=0; i<KMaterial.size(); i++){
newMaterial.nu.push_back(KMaterial[i].nu);
eta = complex<double>(NMaterial[i].A, KMaterial[i].A);
newMaterial.eta.push_back(eta);
}
MaterialList.push_back(newMaterial);
}
void LoadMaterial(string fileNameK, string materialName){
//load the material absorbance
vector<SpecPair> KMaterial = LoadSpectrum(fileNameK.c_str());
vector<SpecPair> NMaterial;
//KMaterial = LoadSpectrum("eta_TolueneK.txt");
//compute the real IR using Kramers Kronig
//copy the absorbance values into a linear array
double* k = (double*)malloc(sizeof(double) * KMaterial.size());
double* n = (double*)malloc(sizeof(double) * KMaterial.size());
for(unsigned int i=0; i<KMaterial.size(); i++)
k[i] = KMaterial[i].A;
//use Kramers Kronig to determine the real part of the index of refraction
cudaKramersKronig(n, k, KMaterial.size(), KMaterial[0].nu, KMaterial.back().nu, baseIR);
SpecPair temp;
for(unsigned int i=0; i<KMaterial.size(); i++)
{
temp.nu = KMaterial[i].nu;
temp.A = n[i];
NMaterial.push_back(temp);
}
//create the material
Material newMaterial;
newMaterial.name = materialName;
complex<double> eta;
for(unsigned int i=0; i<KMaterial.size(); i++){
newMaterial.nu.push_back(KMaterial[i].nu);
eta = complex<double>(NMaterial[i].A, KMaterial[i].A);
newMaterial.eta.push_back(eta);
}
MaterialList.push_back(newMaterial);
}
void LoadSource(string fileNameSource)
{
SourceSpectrum = LoadSpectrum(fileNameSource);
}
void ResampleSource()
{
//clear the current resampled spectrum
SourceResampled.clear();
//get the number of source and material samples
int nMatSamples = EtaK.size();
int nSourceSamples = SourceSpectrum.size();
float nu, I;
for(int i=0; i<nMatSamples; i++)
{
SpecPair newSample;
newSample.nu = EtaK[i].nu;
//iterate through the SourceSpectrum to find the bounding wavelengths
if(newSample.nu < SourceSpectrum[0].nu)
newSample.A = 0.0;
else if(newSample.nu > SourceSpectrum[nSourceSamples-1].nu)
newSample.A = 0.0;
else
{
int k=1;
while(SourceSpectrum[k].nu < newSample.nu)
k++;
//interpolate
float a = (newSample.nu - SourceSpectrum[k-1].nu)/(SourceSpectrum[k].nu - SourceSpectrum[k-1].nu);
newSample.A = a * SourceSpectrum[k].A + (1.0 - a) * SourceSpectrum[k-1].A;
}
//insert the new spectral point into the resampled spectrum
SourceResampled.push_back(newSample);
//cout<<newSample.nu<<" "<<newSample.A<<endl;
}
}
void FitDisplay(){
double minA = 99999.0;
double maxA = -99999.0;
double k, n;
if(dispSimSpec)
for(unsigned int i=0; i<SimSpectrum.size(); i++)
{
if(SimSpectrum[i].A < minA)
minA = SimSpectrum[i].A;
if(SimSpectrum[i].A > maxA)
maxA = SimSpectrum[i].A;
}
if(dispRefSpec && RefSpectrum.size() > 0)
for(unsigned int i=0; i<RefSpectrum[currentSpec].size(); i++)
{
if(RefSpectrum[currentSpec][i].A < minA)
minA = RefSpectrum[currentSpec][i].A;
if(RefSpectrum[currentSpec][i].A > maxA)
maxA = RefSpectrum[currentSpec][i].A;
}
if(dispMatK)
for(unsigned int i=0; i<EtaK.size(); i++)
{
k = MaterialList[currentMaterial].eta[i].imag() * dispScaleK;
if(k < minA)
minA = k;
if(k > maxA)
maxA = k;
}
if(dispSimK)
for(unsigned int i=0; i<EtaK.size(); i++)
{
k = EtaK[i].A * dispScaleK;
if(k < minA)
minA = k;
if(EtaK[i].A > maxA)
maxA = k;
}
if(dispMatN)
for(unsigned int i=0; i<EtaN.size(); i++)
{
n = (MaterialList[currentMaterial].eta[i].real() - baseIR) * dispScaleN;
if(n < minA)
minA = n;
if(n > maxA)
maxA = n;
}
if(dispSimN)
for(unsigned int i=0; i<EtaN.size(); i++)
{
n = (EtaN[i].A - baseIR) * dispScaleN;
if(n < minA)
minA = n;
if(n > maxA)
maxA = n;
}
aMin = minA;
aMax = maxA;
UpdateDisplay();
}
void ChangeAbsorbance(){
//compute the real part of the index of refraction
//copy the absorbance values into a linear array
int nSamples = MaterialList[currentMaterial].eta.size();
double startNu = MaterialList[currentMaterial].nu.front();
double endNu = MaterialList[currentMaterial].nu.back();
double* k = (double*)malloc(sizeof(double) * nSamples);
double* n = (double*)malloc(sizeof(double) * nSamples);
for(int i=0; i<nSamples; i++)
k[i] = MaterialList[currentMaterial].eta[i].imag() * cA;
//NMaterial.clear();
EtaK.clear();
EtaN.clear();
//use Kramers Kronig to determine the real part of the index of refraction
cudaKramersKronig(n, k, nSamples, startNu, endNu, baseIR);
//copy the real part of the index of refraction into the vector
SpecPair temp;
//load the imaginary IR from the absorbance data
double nu;
for(int i=0; i<nSamples; i++){
nu = MaterialList[currentMaterial].nu[i];
if(nu >= nuMin && nu <= nuMax){
temp.nu = nu;
temp.A = k[i];
EtaK.push_back(temp);
//temp.A = NMaterial[i].A;
temp.A = n[i];
EtaN.push_back(temp);
}
}
free(k);
free(n);
}
void SetMaterial()
{
EtaK.clear();
EtaN.clear();
int nSamples = MaterialList[currentMaterial].eta.size();
double nu;
SpecPair temp;
//initialize the current nuMin and nuMax values
nuMin = MaterialList[currentMaterial].nu[0];
nuMax = nuMin;
for(int i=0; i<nSamples; i++){
nu = MaterialList[currentMaterial].nu[i];
//if(nu >= nuMin && nu <= nuMax){
//update the min and max values for display
if(nu < nuMin) nuMin = nu;
if(nu > nuMax) nuMax = nu;
temp.nu = nu;
temp.A = MaterialList[currentMaterial].eta[i].imag();
EtaK.push_back(temp);
temp.A = MaterialList[currentMaterial].eta[i].real();
EtaN.push_back(temp);
}
cA = 1.0;
//resample the source spectrum
if(SourceSpectrum.size() != 0)
ResampleSource();
}
int main(int argc, char *argv[])
{
//load the default project file (any previous optical settings)
LoadState();
//load the default materials
LoadMaterial("eta_TolueneK.txt", "eta_TolueneN.txt", "Toluene");
LoadMaterial("kPMMA.txt", "PMMA");
LoadMaterial("eta_polystyreneK.txt", "Polystyrene");
//LoadMaterial("../../../../data/materials/rtsSU8_k.txt", "../../../../data/materials/rtsSU8_n.txt", "SU8");
SetMaterial();
//load a mid-infrared source
LoadSource("source_midIR.txt");
ResampleSource();
//compute the analytical solution for the Mie scattered spectrum
SimulateSpectrum();
QApplication a(argc, argv);
InteractiveMie w;
w.show() ;
w.move(0, 0);
QSize uiFrame = w.frameSize() + QSize(10, 10);
cout<<"Frame: "<<uiFrame.width()<<endl;
QSize uiNoFrame = w.size();
cout<<"No Frame: "<<uiNoFrame.width()<<endl;
int frameHeight = uiFrame.height() - uiNoFrame.height();
//activate a console for output
RedirectIOToConsole(0, uiFrame.height(), uiFrame.width(), 400);
printf("Frame height: %d\n", frameHeight);
//set the size and position of the spectrum window
int visWinSize = uiFrame.height()/2 - frameHeight;
//create the far field window
gpSpectrumDisplay = new qtSpectrumDisplay();
gpSpectrumDisplay->resize(visWinSize*2, visWinSize);
gpSpectrumDisplay->move(uiFrame.width(), 0);
gpSpectrumDisplay->show();
//distortion dialog box
distortionDialog = new qtDistortionDialog();
distortionDialog->move(0, 0);
//display the distortion map
distortionScene = new QGraphicsScene();
distortionWindow = new QGraphicsView(distortionScene);
distortionWindow->move(uiFrame.width(), visWinSize);
//refresh the UI
w.refreshUI();
return a.exec();
}