main.cpp
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#include <fstream>
#include <iostream>
using namespace std;
#include "interactivemie.h"
#include <QtWidgets/QApplication>
#include <QGraphicsScene>
#include <QGraphicsView>
#include <QGraphicsPixmapItem>
#include <QLayout>
#include "qtSpectrumDisplay.h"
//#include "qwtSpectrumDisplay.h"
#include "globals.h"
#include "rtsGUIConsole.h"
#include "PerformanceData.h"
#include <complex>
#include <sstream>
//#include <direct.h>
PerformanceData PD;
qtSpectrumDisplay* gpSpectrumDisplay;
//qwtSpectrumDisplay* SpectrumDisplay;
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 nMag = 1.0;
double kMax = 1.0;
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 = -1;
//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();
//SpectrumDisplay->replot();
}
void LoadMaterial(string fileName, string materialName)
{
//open the file
ifstream inFile(fileName.c_str());
if(!inFile)
{
cout<<"Error loading material: "<<fileName<<endl;
return;
}
Material newMaterial;
newMaterial.validN = false;
newMaterial.validK = false;
//read the header
string units;
//getline(inFile, units, '\t');
char c = 0;
while(c != '\n')
{
inFile.get(c);
if(c == 'n') newMaterial.validN = true;
if(c == 'k') newMaterial.validK = true;
}
//read the entire refractive index (both real and imaginary)
float nu;
float n;
float k;
while(inFile>>nu)
{
n = 1.0;
k = 0.0;
if(newMaterial.validN)
inFile>>n;
if(newMaterial.validK)
inFile>>k;
//ignore the rest of the line
inFile.ignore();
newMaterial.nu.push_back(nu);
newMaterial.eta.push_back(complex<double>(n, k));
}
//iterate through the material to compute the necessary bounds for display
float minN = 9999;
float maxN = -9999;
float sumN = 0;
float maxK = 0;
for(unsigned int i = 0; i<newMaterial.nu.size(); i++)
{
n = newMaterial.eta[i].real();
k = newMaterial.eta[i].imag();
if(n < minN) minN = n;
if(n > maxN) maxN = n;
if(k > maxK) maxK = k;
sumN += n;
}
float meanN = sumN / newMaterial.nu.size();
nMag = max(maxN - meanN, meanN - minN);
kMax = maxK;
baseIR = meanN;
//set the name of the material object
newMaterial.name = materialName;
//add it to the material list
MaterialList.push_back(newMaterial);
currentMaterial = MaterialList.size() - 1;
}
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();
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();
if(currentMaterial == -1) return;
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("etaToluene.txt", "Toluene");
//LoadMaterial("kPolystyrene.txt", "Polystyrene");
LoadMaterial("etaPolystyrene.txt", "Polystyrene");
LoadMaterial("etaPMMA.txt", "PMMA");
//LoadMaterial("kPMMA.txt", "PMMA");
//LoadMaterial("kPolyethylene.txt", "Polyethylene");
//LoadMaterial("kPTFE.txt", "Teflon");
//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);
//SpectrumDisplay = new qwtSpectrumDisplay();
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();
}