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//AnyOption for command-line processing
//#include "anyoption.h"
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#include "rts/optics/material.h"
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#include "nearfield.h"
#include "microscope.h"
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#include "rts/visualization/colormap.h"
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#include "fileout.h"
//extern nearfieldStruct* NF;
extern microscopeStruct* SCOPE;
extern fileoutStruct gFileOut;
//default values
#include "defaults.h"
#include <string>
#include <sstream>
#include <fstream>
#include <limits>
using namespace std;
#include <boost/program_options.hpp>
namespace po = boost::program_options;
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extern bool verbose;
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extern bool gui;
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static void lNearfield(po::variables_map vm)
{
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//test to see if we are running a vector field simulation
bool vectorField = false;
if(vm.count("vector"))
vectorField = true;
SCOPE->scalarSim = !vectorField;
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//test to see if we are simulating a plane wave
bool planeWave = DEFAULT_PLANEWAVE;
if(vm.count("plane-wave"))
planeWave = !planeWave;
SCOPE->nf.planeWave = planeWave;
//get the incident field amplitude
SCOPE->nf.A = vm["amplitude"].as<ptype>();
//get the condenser parameters
SCOPE->nf.condenser[0] = DEFAULT_CONDENSER_MIN;
SCOPE->nf.condenser[1] = DEFAULT_CONDENSER_MAX;
if(vm.count("condenser"))
{
vector<ptype> cparams = vm["condenser"].as< vector<ptype> >();
if(cparams.size() == 1)
SCOPE->nf.condenser[1] = cparams[0];
else
{
SCOPE->nf.condenser[0] = cparams[0];
SCOPE->nf.condenser[1] = cparams[1];
}
}
//get the focal rtsPoint position
SCOPE->nf.focus[0] = DEFAULT_FOCUS_X;
SCOPE->nf.focus[1] = DEFAULT_FOCUS_Y;
SCOPE->nf.focus[2] = DEFAULT_FOCUS_Z;
if(vm.count("focus"))
{
vector<ptype> fpos = vm["focus"].as< vector<ptype> >();
if(fpos.size() != 3)
{
cout<<"BIMSIM Error - the incident focal point is incorrectly specified; it must have three components."<<endl;
exit(1);
}
SCOPE->nf.focus[0] = fpos[0];
SCOPE->nf.focus[1] = fpos[1];
SCOPE->nf.focus[2] = fpos[2];
}
//get the incident light direction (k-vector)
bsVector spherical(1, 0, 0);
//if a k-vector is specified
if(vm.count("k"))
{
vector<ptype> kvec = vm["k"].as< vector<ptype> >();
if(kvec.size() != 2)
{
cout<<"BIMSIM Error - k-vector is not specified correctly: it must contain two elements"<<endl;
exit(1);
}
spherical[1] = kvec[0];
spherical[2] = kvec[1];
}
SCOPE->nf.k = spherical.sph2cart();
//incident field order
SCOPE->nf.m = vm["field-order"].as<int>();
//number of Monte-Carlo samples
SCOPE->nf.nWaves = vm["samples"].as<int>();
//random number seed for Monte-Carlo samples
if(vm.count("seed"))
srand(vm["seed"].as<unsigned int>());
}
static void loadOutputParams(po::variables_map vm)
{
//append simulation results to previous binary files
gFileOut.append = DEFAULT_APPEND;
if(vm.count("append"))
gFileOut.append = true;
//image parameters
//component of the field to be saved
std::string fieldStr;
fieldStr = vm["output-type"].as<string>();
if(fieldStr == "magnitude")
gFileOut.field = fileoutStruct::fieldMag;
else if(fieldStr == "intensity")
gFileOut.field = fileoutStruct::fieldIntensity;
else if(fieldStr == "polarization")
gFileOut.field = fileoutStruct::fieldPolar;
else if(fieldStr == "imaginary")
gFileOut.field = fileoutStruct::fieldImag;
else if(fieldStr == "real")
gFileOut.field = fileoutStruct::fieldReal;
else if(fieldStr == "angular-spectrum")
gFileOut.field = fileoutStruct::fieldAngularSpectrum;
//image file names
gFileOut.intFile = vm["intensity"].as<string>();
gFileOut.absFile = vm["absorbance"].as<string>();
gFileOut.transFile = vm["transmittance"].as<string>();
gFileOut.nearFile = vm["near-field"].as<string>();
gFileOut.farFile = vm["far-field"].as<string>();
//colormap
std::string cmapStr;
cmapStr = vm["colormap"].as<string>();
if(cmapStr == "brewer")
gFileOut.colormap = rts::cmBrewer;
else if(cmapStr == "gray")
gFileOut.colormap = rts::cmGrayscale;
else
cout<<"color-map value not recognized (using default): "<<cmapStr<<endl;
}
void lFlags(po::variables_map vm, po::options_description desc)
{
//display help and exit
if(vm.count("help"))
{
cout<<desc<<endl;
exit(1);
}
//flag for verbose output
if(vm.count("verbose"))
verbose = true;
if(vm.count("recursive"))
{
SCOPE->nf.lut_us = false;
SCOPE->nf.lut_uf = false;
}
else if(vm.count("recursive-us"))
{
SCOPE->nf.lut_us = false;
}
else if(vm.count("lut-uf"))
{
SCOPE->nf.lut_uf = true;
}
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//gui
if(vm.count("gui"))
gui = true;
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}
void lWavelength(po::variables_map vm)
{
//load the wavelength
if(vm.count("nu"))
{
//wavelength is given in wavenumber - transform and flag
SCOPE->nf.lambda = 10000/vm["nu"].as<ptype>();
gFileOut.wavenumber = true;
}
//otherwise we are using lambda = wavelength
else
{
SCOPE->nf.lambda = vm["lambda"].as<ptype>();
gFileOut.wavenumber = false;
}
}
static void lSpheres(string sphereList)
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{
/*This function loads a list of sphere given in the string sphereList
The format is:
x y z a m
where
x, y, z = sphere position (required)
a = sphere radius (required)
m = material ID (optional) */
std::stringstream ss(sphereList);
while(!ss.eof())
{
//create a new sphere
sphere newS;
//get the sphere data
ss>>newS.p[0];
ss>>newS.p[1];
ss>>newS.p[2];
ss>>newS.a;
if(ss.peek() != '\n')
ss>>newS.iMaterial;
//add the new sphere to the sphere vector
SCOPE->nf.sVector.push_back(newS);
//ignore the rest of the line
ss.ignore(std::numeric_limits<std::streamsize>::max(), '\n');
//check out the next element (this should set the EOF error flag)
ss.peek();
}
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}
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void lSpheres(po::variables_map vm)
{
//if a sphere is specified at the command line
if(vm.count("spheres"))
{
//convert the sphere to a string
vector<ptype> sdesc = vm["spheres"].as< vector<ptype> >();
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//compute the number of spheres specified
unsigned int nS;
if(sdesc.size() <= 5)
nS = 1;
else
{
//if the number of parameters is divisible by 4, compute the number of spheres
if(sdesc.size() % 5 == 0)
nS = sdesc.size() / 5;
else
{
cout<<"BIMSIM Error: Invalid number of sphere parameters."<<endl;
exit(1);
}
}
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stringstream ss;
//for each sphere
for(unsigned int s=0; s<nS; s++)
{
//compute the number of sphere parameters
unsigned int nP;
if(nS == 1) nP = sdesc.size();
else nP = 5;
//store each parameter as a string
for(unsigned int i=0; i<nP; i++)
{
ss<<sdesc[s*5 + i]<<" ";
}
ss<<endl;
}
//convert the string to a sphere list
lSpheres(ss.str());
}
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//if a files are specified
if(vm.count("sphere-file"))
{
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vector<string> filenames = vm["sphere-file"].as< vector<string> >();
//load each file
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for(unsigned int iS=0; iS<filenames.size(); iS++)
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{
//load the file into a string
std::ifstream ifs(filenames[iS].c_str());
if(!ifs)
{
cout<<"Error loading sphere file."<<endl;
exit(1);
}
std::string instr((std::istreambuf_iterator<char>(ifs)), std::istreambuf_iterator<char>());
//load the list of spheres from a string
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lSpheres(instr);
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}
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//make sure the appropriate materials are loaded
unsigned int nS = SCOPE->nf.sVector.size();
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//for each sphere
for(unsigned int s = 0; s<nS; s++)
{
//make sure the corresponding material exists
if(SCOPE->nf.sVector[s].iMaterial + 1 > SCOPE->nf.mVector.size())
{
//otherwise output an error
cout<<"BIMSIM Error - A material is not loaded for sphere "<<s+1<<"."<<endl;
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cout<<"Material requested: "<<SCOPE->nf.sVector[s].iMaterial + 1<<endl;
cout<<"Number of materials: "<<SCOPE->nf.mVector.size()<<endl;
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exit(1);
}
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}
}
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static void lMaterials(po::variables_map vm)
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{
//if materials are specified at the command line
if(vm.count("materials"))
{
vector<ptype> matVec = vm["materials"].as< vector<ptype> >();
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if(matVec.size() == 1)
{
rts::material<ptype> newM(SCOPE->nf.lambda, matVec[0], 0);
SCOPE->nf.mVector.push_back(newM);
}
else if(matVec.size() %2 != 0)
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{
cout<<"BIMSim Error: materials must be specified in n, k pairs"<<endl;
exit(1);
}
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else
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{
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for(unsigned int i=0; i<matVec.size(); i+=2)
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{
rts::material<ptype> newM(SCOPE->nf.lambda, matVec[i], matVec[i+1]);
SCOPE->nf.mVector.push_back(newM);
}
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}
}
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//if file names are specified, load the materials
if(vm.count("material-file"))
{
vector<string> filenames = vm["material-file"].as< vector<string> >();
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for(unsigned int i=0; i<filenames.size(); i++)
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{
//load the file into a string
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//std::ifstream ifs(filenames[i].c_str());
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//std::string instr((std::istreambuf_iterator<char>(ifs)), std::istreambuf_iterator<char>());
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//load the list of spheres from a string
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rts::material<ptype> newM(filenames[i].c_str());
//newM.fromStr(instr, "");
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SCOPE->nf.mVector.push_back(newM);
}
}
}
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static void lOptics(po::variables_map vm)
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{
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SCOPE->objective[0] = DEFAULT_OBJECTIVE_MIN;
SCOPE->objective[1] = DEFAULT_OBJECTIVE_MAX;
if(vm.count("objective"))
{
vector<ptype> oparams = vm["objective"].as< vector<ptype> >();
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if(oparams.size() == 1)
SCOPE->objective[1] = oparams[0];
else
{
SCOPE->objective[0] = oparams[0];
SCOPE->objective[1] = oparams[1];
}
}
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}
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static void lImagePlane(po::variables_map vm)
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{
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bsPoint pMin(DEFAULT_PLANE_MIN_X, DEFAULT_PLANE_MIN_Y, DEFAULT_PLANE_MIN_Z);
bsPoint pMax(DEFAULT_PLANE_MAX_X, DEFAULT_PLANE_MAX_Y, DEFAULT_PLANE_MAX_Z);
bsVector normal(DEFAULT_PLANE_NORM_X, DEFAULT_PLANE_NORM_Y, DEFAULT_PLANE_NORM_Z);
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//set the default values for the slice position and orientation
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if(vm.count("plane-lower-left") && vm.count("plane-upper-right") && vm.count("plane-normal"))
{
vector<ptype> ll = vm["plane-lower-left"].as< vector<ptype> >();
if(ll.size() != 3)
{
cout<<"BIMSIM Error - The lower-left corner of the image plane is incorrectly specified."<<endl;
exit(1);
}
vector<ptype> ur = vm["plane-lower-left"].as< vector<ptype> >();
if(ur.size() != 3)
{
cout<<"BIMSIM Error - The upper-right corner of the image plane is incorrectly specified."<<endl;
exit(1);
}
vector<ptype> norm = vm["plane-lower-left"].as< vector<ptype> >();
if(norm.size() != 3)
{
cout<<"BIMSIM Error - The normal of the image plane is incorrectly specified."<<endl;
exit(1);
}
pMin = bsPoint(ll[0], ll[1], ll[2]);
pMax = bsPoint(ur[0], ur[1], ur[2]);
normal = bsVector(norm[0], norm[1], norm[2]);
}
else if(vm.count("xy"))
{
//default plane size in microns
ptype s = DEFAULT_PLANE_SIZE;
ptype pos = DEFAULT_PLANE_POSITION;
vector<ptype> xy = vm["xy"].as< vector<ptype> >();
if(xy.size() >= 1)
s = xy[0];
if(xy.size() >= 2)
pos = xy[1];
//calculate the plane corners and normal based on the size and position
pMin = bsPoint(-s/2, -s/2, pos);
pMax = bsPoint(s/2, s/2, pos);
normal = bsVector(0, 0, 1);
}
else if(vm.count("xz"))
{
//default plane size in microns
ptype size = DEFAULT_PLANE_SIZE;
ptype pos = DEFAULT_PLANE_POSITION;
vector<ptype> xz = vm["xz"].as< vector<ptype> >();
if(xz.size() >= 1)
size = xz[0];
if(xz.size() >= 2)
pos = xz[1];
//calculate the plane corners and normal based on the size and position
pMin = bsPoint(-size/2, pos, -size/2);
pMax = bsPoint(size/2, pos, size/2);
normal = bsVector(0, -1, 0);
}
else if(vm.count("yz"))
{
//default plane size in microns
ptype size = DEFAULT_PLANE_SIZE;
ptype pos = DEFAULT_PLANE_POSITION;
vector<ptype> yz = vm["yz"].as< vector<ptype> >();
if(yz.size() >= 1)
size = yz[0];
if(yz.size() >= 2)
pos = yz[1];
//calculate the plane corners and normal based on the size and position
pMin = bsPoint(pos, -size/2, -size/2);
pMax = bsPoint(pos, size/2, size/2);
normal = bsVector(1, 0, 0);
}
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SCOPE->setPos(pMin, pMax, normal);
//resolution
SCOPE->setRes(vm["resolution"].as<unsigned int>(),
vm["resolution"].as<unsigned int>(),
vm["padding"].as<unsigned int>(),
vm["supersample"].as<unsigned int>());
SCOPE->setNearfield();
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}
static void OutputOptions()
{
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cout<<SCOPE->toStr();
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cout<<"# of source points: "<<SCOPE->focalPoints.size()<<endl;
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}
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vector<ptype> test;
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static void SetOptions(po::options_description &desc)
{
desc.add_options()
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("help", "prints this help")
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("gui", "run using the Qt GUI")
("verbose", "verbose output\n\nOutput Parameters\n--------------------------")
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("vector", "run a vector field simulation")
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("intensity", po::value<string>()->default_value(DEFAULT_INTENSITY_FILE), "output measured intensity (filename)")
("absorbance", po::value<string>()->default_value(DEFAULT_ABSORBANCE_FILE), "output measured absorbance (filename)")
("transmittance", po::value<string>()->default_value(DEFAULT_TRANSMITTANCE_FILE), "output measured transmittance (filename)")
("far-field", po::value<string>()->default_value(DEFAULT_FAR_FILE), "output far-field at detector (filename)")
("near-field", po::value<string>()->default_value(DEFAULT_NEAR_FILE), "output field at focal plane (filename)")
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("extended-source", po::value<string>()->default_value(DEFAULT_EXTENDED_SOURCE), "image of source at focus (filename)")
("output-type", po::value<string>()->default_value(DEFAULT_FIELD_TYPE), "output field value:\n magnitude, polarization, real, imaginary, angular-spectrum")
("colormap", po::value<string>()->default_value(DEFAULT_COLORMAP), "colormap: gray, brewer")
("append", "append result to an existing file\n (binary files only)\n\nSphere Parameters\n--------------------------")
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("spheres", po::value< vector<ptype> >()->multitoken(), "sphere position: x y z a m")
("sphere-file", po::value< vector<string> >()->multitoken(), "sphere file:\n [x y z radius material]")
("materials", po::value< vector<ptype> >()->multitoken(), "refractive indices as n, k pairs:\n ex. -m n0 k0 n1 k1 n2 k2")
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("material-file", po::value< vector<string> >()->multitoken(), "material file:\n [lambda n k]\n\nOptics\n--------------------------")
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("lambda", po::value<ptype>()->default_value(DEFAULT_LAMBDA), "incident wavelength")
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("nu", po::value<ptype>(), "incident frequency (in cm^-1)\n(if specified, lambda is ignored)")
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("k", po::value< vector<ptype> >()->multitoken(), "k-vector direction: -k theta phi\n theta = [0 2*pi], phi = [0 pi]")
("amplitude", po::value<ptype>()->default_value(DEFAULT_AMPLITUDE), "incident field amplitude")
("condenser", po::value< vector<ptype> >()->multitoken(), "condenser numerical aperature\nA pair of values can be used to specify an inner obscuration: -c NAin NAout")
("objective", po::value< vector<ptype> >()->multitoken(), "objective numerical aperature\nA pair of values can be used to specify an inner obscuration: -c NAin NAout")
("focus", po::value< vector<ptype> >()->multitoken(), "focal position for the incident point source\n (default = --focus 0 0 0)")
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("plane-wave", "simulates an incident plane wave\n\n\nImaging Parameters\n--------------------------")
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("resolution", po::value<unsigned int>()->default_value(DEFAULT_SLICE_RES), "resolution of the detector")
("plane-lower-left", po::value< vector<ptype> >()->multitoken(), "lower-left position of the image plane")
("plane-upper-right", po::value< vector<ptype> >()->multitoken(), "upper-right position of the image plane")
("plane-normal", po::value< vector<ptype> >()->multitoken(), "normal for the image plane")
("xy", po::value< vector<ptype> >()->multitoken(), "specify an x-y image plane\n (standard microscope)")
("xz", po::value< vector<ptype> >()->multitoken(), "specify a x-z image plane\n (cross-section of the focal volume)")
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("yz", po::value< vector<ptype> >()->multitoken(), "specify a y-z image plane\n (cross-section of the focal volume)\n\nSampling Parameters\n--------------------------")
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("samples", po::value<int>()->default_value(DEFAULT_SAMPLES), "Monte-Carlo samples used to compute Us")
("padding", po::value<unsigned int>()->default_value(DEFAULT_PADDING), "FFT padding for the objective bandpass")
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("supersample", po::value<unsigned int>()->default_value(DEFAULT_SUPERSAMPLE), "super-sampling rate for the detector field")
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("field-order", po::value<int>()->default_value(DEFAULT_FIELD_ORDER), "order of the incident field")
("seed", po::value<unsigned int>(), "seed for the Monte-Carlo random number generator")
("recursive", "evaluate all Bessel functions recursively\n")
("recursive-us", "evaluate scattered-field Bessel functions recursively\n")
("lut-uf", "evaluate the focused-field using a look-up table\n")
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;
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}
static void LoadParameters(int argc, char *argv[])
{
//create an option description
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po::options_description desc("BimSim arguments");
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//fill it with options
SetOptions(desc);
po::variables_map vm;
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po::store(po::parse_command_line(argc, argv, desc, po::command_line_style::unix_style ^ po::command_line_style::allow_short), vm);
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po::notify(vm);
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//load flags (help, verbose output)
lFlags(vm, desc);
//load the wavelength
lWavelength(vm);
//load materials
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lMaterials(vm);
//load the sphere data
lSpheres(vm);
//load the optics
lOptics(vm);
//load the position and orientation of the image plane
lImagePlane(vm);
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lNearfield(vm);
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loadOutputParams(vm);
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//if an extended source will be used
if(vm["extended-source"].as<string>() != "")
{
//load the point sources
string filename = vm["extended-source"].as<string>();
SCOPE->LoadExtendedSource(filename);
}
}
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