main.cpp
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//Update the data output format in example_layer().
#include "layer.h"
#include <windows.h>
#include <fstream>
#include <iostream>
#include "stim/parser/arguments.h"
using namespace std;
#define PI 3.14159265358979323846264338328
bool ASCII_output = false;
bool CPU_op = false;
void advertise() {
std::cout << std::endl << std::endl;
std::cout << "=========================================================================" << std::endl;
//std::cout << "Thank you for using the NetMets network comparison tool!" << std::endl;
std::cout << "Scalable Tissue Imaging and Modeling (STIM) Lab, University of Houston" << std::endl;
std::cout << "=========================================================================" << std::endl << std::endl;
}
//Calculate Ez from vector d and Ex Ey.
void E_Cal(vector<complex<double>>* E, vector<complex<double>>* d) {
if (d->size() == 2) {
complex<double> dz = sqrt(1.0 + 0i - pow((*d)[0], 2) - pow((*d)[1], 2));
d->push_back(dz);
}
E->push_back(-((*E)[0] * (*d)[0] + (*E)[1] * (*d)[1]) / (*d)[2]);
}
void output_binary(std::string filename, layersample& layers) {
size_t L = layers.n.size(); // get the number of layers
std::ofstream outFile;
outFile.open(filename, std::ofstream::binary); // open the output file for binary writing
if (outFile) {
outFile.write((char*)&layers.k, sizeof(double));
outFile.write((char*)&layers.d[0], sizeof(double));
outFile.write((char*)&layers.d[1], sizeof(double));
outFile.write((char*)&layers.n[0], sizeof(double) * 2);
for (size_t i = 0; i < L; i++) {
outFile.write((char*)&layers.z[i], sizeof(double));
outFile.write((char*)&layers.sz[i], 2 * sizeof(double));
outFile.write((char*)&layers.Pt[i], 2 * sizeof(double));
outFile.write((char*)&layers.Pt[i + L], 2 * sizeof(double));
outFile.write((char*)&layers.Pt[i + 2 * L], 2 * sizeof(double));
outFile.write((char*)&layers.Pr[i], 2 * sizeof(double));
outFile.write((char*)&layers.Pr[i + L], 2 * sizeof(double));
outFile.write((char*)&layers.Pr[i + 2 * L], 2 * sizeof(double));
}
outFile.close();
}
else {
std::cout << "ERROR opening output file for binary writing: " << filename << std::endl;
}
}
void output_txt(std::string filename, layersample& layers) {
size_t L = layers.n.size(); // get the number of layers
std::ofstream outFile;
outFile.open(filename); // open the output file for text writing
if (!outFile) {
std::cout << "ERROR: Could not open file " << filename << std::endl;
exit(1);
}
int width = 15;
outFile << "--------------------------------" << endl;
outFile << "The wavenumber at free space is : " << layers.k << endl;
for (size_t i = 0; i < L; i++) {
if (i == 0) {
outFile << "--------------------------------" << endl;
outFile << "LAYER " << i << " (z = " << layers.z[i] << ")" << endl;
outFile << "refractive index: " << layers.n[i].real() << " + i " << layers.n[i].imag() << endl;
outFile << "----------------------" << endl;
outFile << "sx = " << setw(width) << layers.s[0].real() << " + i " << layers.s[0].imag() << endl;
outFile << "sy = " << setw(width) << layers.s[1].real() << " + i " << layers.s[1].imag() << endl;
outFile << "sz = " << setw(width) << layers.sz[i].real() << " + i " << layers.sz[i].imag() << endl;
outFile << "----->>>>>" << endl;
outFile << " X = " << setw(width) << layers.Pt[i].real() << " + i " << layers.Pt[i].imag() << endl;
outFile << " Y = " << setw(width) << layers.Pt[i + L].real() << " + i " << layers.Pt[i + L].imag() << endl;
outFile << " Z = " << setw(width) << layers.Pt[i + 2 * L].real() << " + i " << layers.Pt[i + 2 * L].imag() << endl;
outFile << "<<<<<-----" << endl;
outFile << " X = " << setw(width) << layers.Pr[i].real() << " + i " << layers.Pr[i].imag() << endl;
outFile << " Y = " << setw(width) << layers.Pr[i + L].real() << " + i " << layers.Pr[i + L].imag() << endl;
outFile << " Z = " << setw(width) << layers.Pr[i + 2 * L].real() << " + i " << layers.Pr[i + 2 * L].imag() << endl;
}
else {
outFile << "----------------------" << endl;
outFile << "LAYER " << i << " (z = " << layers.z[i] << ")" << endl;
outFile << "refractive index: " << layers.n[i].real() << " + i " << layers.n[i].imag() << endl;
outFile << "----------------------" << endl;
outFile << "sx = " << setw(width) << layers.s[0].real() << " + i " << layers.s[0].imag() << endl;
outFile << "sy = " << setw(width) << layers.s[1].real() << " + i " << layers.s[1].imag() << endl;
outFile << "sz = " << setw(width) << layers.sz[i].real() << " + i " << layers.sz[i].imag() << endl;
outFile << "----->>>>>" << endl;
outFile << " X = " << setw(width) << layers.Pt[i].real() << " + i " << layers.Pt[i].imag() << endl;
outFile << " Y = " << setw(width) << layers.Pt[i + L].real() << " + i " << layers.Pt[i + L].imag() << endl;
outFile << " Z = " << setw(width) << layers.Pt[i + 2 * L].real() << " + i " << layers.Pt[i + 2 * L].imag() << endl;
outFile << "<<<<<-----" << endl;
outFile << " X = " << setw(width) << layers.Pr[i].real() << " + i " << layers.Pr[i].imag() << endl;
outFile << " Y = " << setw(width) << layers.Pr[i + L].real() << " + i " << layers.Pr[i + L].imag() << endl;
outFile << " Z = " << setw(width) << layers.Pr[i + 2 * L].real() << " + i " << layers.Pr[i + 2 * L].imag() << endl;
}
}
outFile.close();
}
void calculate_layer(std::string outName,
vector<complex<double>>* ns, // the refractive index.
vector<double>* depths, // z-direction position.
vector<complex<double>>* E0, // the initialized E0.
vector<complex<double>>* d0, // direction of propagation of the plane wave.
double k0) { // the wavenumber at free space.
std::string outName_ext(outName, size(outName)-4, size(outName)-1); // extract the extension of the output file
E_Cal(E0, d0); // make sure that both vectors are orthogonal.
//Creat a new layersample and initialize.
layersample Layer1; // create a layered sample
Layer1.n = *ns; // set a pointer to the refractive indices
Layer1.z = *depths; // set a pointer to the layer depths
Layer1.d = *d0;
Layer1.k = k0;
LARGE_INTEGER t1, t2, tc; // Timing.
QueryPerformanceFrequency(&tc);
QueryPerformanceCounter(&t1);
Layer1.solve(E0, CPU_op); // Solve for the substrate field in GPU.
QueryPerformanceCounter(&t2);
std::cout << "time for 'solving linear functions':" << (t2.QuadPart - t1.QuadPart) / (double)tc.QuadPart << "ms."<< std::endl;
//output(outName, Layer1);
if (ASCII_output)
output_txt(outName, Layer1);
else
output_binary(outName, Layer1);
}
//Main function for example_layer.
int main(int argc, char* argv[]) {
stim::arglist args;
//Basic argument lists.
args.add("help", "prints this help");
args.add("s", "propagation direction vector (x, y)", "0.5 0.0", "[-1.0, 1.0]");
args.add("l", "wavelength", "5.0", "in arbitrary units (ex. um)");
args.add("Ex", "complex amplitude (x direction)", "0.5 0.0");
args.add("Ey", "complex amplitude (y direction)", "0.5 0.0");
args.add("z", "layer positions");
args.add("n", "layer optical path length (real refractive index)", "1.0 1.4 1.4 1.0");
args.add("kappa", "layer absorbance (imaginary refractive index)");
args.add("ascii", "output as an ASCII file");
args.add("CPU", "execute the program in CPU");
args.parse(argc, argv);
if (args["help"].is_set()) { // test for help
advertise(); // output the advertisement
std::cout << args.str(); // output arguments
exit(1); // exit
}
ASCII_output = args["ascii"]; // if the ascii flag is set, output an ascii file
CPU_op = args["CPU"]; // if the CPU_op is set, run the program in CPU.
std::string outName;
if (args.nargs() == 1) {
outName = args.arg(0);
}
else if (args.nargs() == 0) {
if (ASCII_output)
outName = "output.txt";
else
outName = "output.lyr";
}
else {
std::cout << "ERROR: Too many arguments." << std::endl;
exit(1);
}
vector<complex<double>> d; //direction of propagation of the plane wave Init: {0.5, 0}
if (args["s"].nargs() == 2) {
d.push_back({ (double)args["s"].as_float(0), 0 });
d.push_back({ (double)args["s"].as_float(1), 0 });
}
double l0 = (double)args["l"].as_float(0); //wavelength.Init: l0 = 5;
double k0 = 2 * PI / l0; //Calculate the free-space wavenumber.
complex<double> Ex = { (double)args["Ex"].as_float(0), (double)args["Ex"].as_float(1) }; //Input E. Init: {1, 1, 0}
complex<double> Ey = { (double)args["Ey"].as_float(0), (double)args["Ey"].as_float(1) };
vector<complex<double>> E0;
E0.push_back(Ex);
E0.push_back(Ey);
//const int LAYERS = args["L"].as_int(); //LAYERS Init: 4
vector<double> depths;
vector<complex<double>> ns;
size_t i = 0;
while(args["n"].is_set() && args["n"].as_float(i)!=0) { //n is the real part.
if (args["kappa"].is_set()) //kappa is the imaginary part.
ns.push_back({ (double)args["n"].as_float(i), (double)args["kappa"].as_float(i) });
else
ns.push_back({ (double)args["n"].as_float(i), 0 }); //ns <- n + i * kappa
i++;
}
for (size_t j = 0; j < i; j++)
if (args["z"].is_set())
depths.push_back((double)args["z"].as_float(i));
else {
depths.push_back((double)-100 + j * 200 / i);
}
/*---------------------------------------example_layer--------------------------------------------*/
calculate_layer(outName, &ns, &depths, &E0, &d, k0);
return 0;
std::cin.get();
}