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options.h 13 KB
3f56f1f9   dmayerich   initial commit
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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"
  #include "colormap.h"
  #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;
  
  static void loadSpheres(string sphereList)
  {
      /*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();
      }
  
  
  
  }
  
  static void loadSpheres(po::variables_map vm)
  {
      //if a files are specified
      if(vm.count("sphere-file"))
      {
          cout<<"Sphere files detected."<<endl;
          vector<string> filenames = vm["sphere-file"].as< vector<string> >();
          //load each file
          for(int iS=0; iS<filenames.size(); iS++)
          {
              //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
              loadSpheres(instr);
          }
      }
  
      //load the sphere from the command line
      if(vm.count("sx") || vm.count("sy") || vm.count("sz") || vm.count("s"))
      {
          //create a new sphere
          sphere newS;
  
  		//set defaults
  		if(vm.count("sx"))
              newS.p[0] = vm["sx"].as<ptype>();
          else
              newS.p[0] = DEFAULT_SPHERE_X;
  
  
  		if(vm.count("sy"))
              newS.p[1] = vm["sy"].as<ptype>();
          else
              newS.p[1] = DEFAULT_SPHERE_Y;
  
  		if(vm.count("sz"))
              newS.p[2] = vm["sz"].as<ptype>();
          else
              newS.p[2] = DEFAULT_SPHERE_Z;
  
  		if(vm.count("radius"))
              newS.a = vm["radius"].as<ptype>();
          else
              newS.a = DEFAULT_SPHERE_A;
  
          //add the sphere to the sphere vector
          SCOPE->nf.sVector.push_back(newS);
  
      }
  }
  
  static void loadMaterials(po::variables_map vm)
  {
  	//if materials are specified at the command line
  	if(vm.count("materials"))
  	{
  		vector<ptype> matVec = vm["materials"].as< vector<ptype> >();
  		if(matVec.size() %2 != 0)
  		{
  			cout<<"BIMSim Error: materials must be specified in n, k pairs"<<endl;
  			exit(1);
  		}
  
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  		for(int i=0; i<matVec.size(); i+=2)
  		{
  			rts::material<ptype> newM(vm["lambda"].as<ptype>(), matVec[i], matVec[i+1]);
  			SCOPE->nf.mVector.push_back(newM);
  		}
  	}
  	else
  	{
  		//add the command line material as the default (material 0)
  		rts::material<ptype> newM(vm["lambda"].as<ptype>(), vm["n"].as<ptype>(), vm["k"].as<ptype>());
  		SCOPE->nf.mVector.push_back(newM);
  	}
  
  	//if file names are specified, load the materials
  	if(vm.count("material-file"))
  	{
          vector<string> filenames = vm["material-file"].as< vector<string> >();
          for(int i=0; i<filenames.size(); i++)
          {
              //load the file into a string
              std::ifstream ifs(filenames[i].c_str());
  
              std::string instr((std::istreambuf_iterator<char>(ifs)), std::istreambuf_iterator<char>());
  
              //load the list of spheres from a string
              rts::material<ptype> newM;
              newM.fromStr(instr, "");
              SCOPE->nf.mVector.push_back(newM);
          }
  	}
  
  }
  
  static void loadNearfieldParams(po::variables_map vm)
  {
  	//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 wavelength
      SCOPE->nf.lambda = vm["lambda"].as<ptype>();
  
  	//get the incident field amplitude
  	SCOPE->nf.A = vm["amplitude"].as<ptype>();
  
  	//get the condenser parameters
      SCOPE->nf.condenser[0] = vm["condenser-min"].as<ptype>();
      SCOPE->nf.condenser[1] = vm["condenser-max"].as<ptype>();
  
  
  	//get the focal rtsPoint position
      SCOPE->nf.focus[0] = vm["fx"].as<ptype>();
      SCOPE->nf.focus[1] = vm["fy"].as<ptype>();
      SCOPE->nf.focus[2] = vm["fz"].as<ptype>();
  
  	//get the incident light direction (k-vector)
  	bsVector spherical;
  	spherical[0] = 1.0;
      spherical[1] = vm["theta"].as<ptype>();
      spherical[2] = vm["phi"].as<ptype>();
  	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>();
  
  
  
  }
  
  static void loadSliceParams(po::variables_map vm)
  {
      //parameters for the sample plane
  
  
  	//set the default values for the slice position and orientation
  	bsPoint pMin(vm["plane-min-x"].as<ptype>(), vm["plane-min-y"].as<ptype>(), vm["plane-min-z"].as<ptype>());
  	bsPoint pMax(vm["plane-max-x"].as<ptype>(), vm["plane-max-y"].as<ptype>(), vm["plane-max-z"].as<ptype>());
  	bsVector normal(vm["plane-norm-x"].as<ptype>(), vm["plane-norm-y"].as<ptype>(), vm["plane-norm-z"].as<ptype>());
  	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();
  
  
  
  }
  
  static void loadMicroscopeParams(po::variables_map vm)
  {
      //objective
      SCOPE->objective[0] = vm["objective-min"].as<ptype>();
      SCOPE->objective[1] = vm["objective-max"].as<ptype>();
  
  
  
  
  
  }
  
  static void loadOutputParams(po::variables_map vm)
  {
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      //append simulation results to previous binary files
      gFileOut.append = DEFAULT_APPEND;
      if(vm.count("append"))
          gFileOut.append = true;
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  	//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::colormap::cmBrewer;
      else if(cmapStr == "gray")
          gFileOut.colormap = rts::colormap::cmGrayscale;
      else
          cout<<"color-map value not recognized (using default): "<<cmapStr<<endl;
  }
  
  static void OutputOptions()
  {
  	cout<<SCOPE->nf.toStr();
  
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  	cout<<"# of source points: "<<SCOPE->focalPoints.size()<<endl;
  
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  }
  
  static void SetOptions(po::options_description &desc)
  {
  	desc.add_options()
  		("help,h", "prints this help")
  		("plane-wave,P", "simulates an incident plane wave")
  		("intensity,I", po::value<string>()->default_value(DEFAULT_INTENSITY_FILE), "output measured intensity (filename)")
  		("absorbance,A", po::value<string>()->default_value(DEFAULT_ABSORBANCE_FILE), "output measured absorbance (filename)")
  		("transmittance,T", po::value<string>()->default_value(DEFAULT_TRANSMITTANCE_FILE), "output measured transmittance (filename)")
  		("far-field,F", po::value<string>()->default_value(DEFAULT_FAR_FILE), "output far-field at detector (filename)")
  		("near-field,N", po::value<string>()->default_value(DEFAULT_NEAR_FILE), "output field at focal plane (filename)")
  		("extended-source,X", po::value<string>()->default_value(DEFAULT_EXTENDED_SOURCE), "image of source at focus (filename)")
  		//("sx,x", po::value<ptype>()->default_value(DEFAULT_SPHERE_X), "sphere coordinates")
  		//("sy,y", po::value<ptype>()->default_value(DEFAULT_SPHERE_Y))
  		//("sz,z", po::value<ptype>()->default_value(DEFAULT_SPHERE_Z))
  		("sx,x", po::value<ptype>(), "sphere coordinates")
  		("sy,y", po::value<ptype>())
  		("sz,z", po::value<ptype>())
  		("radius,r", po::value<ptype>()->default_value(DEFAULT_SPHERE_A), "sphere radius")
  		("samples,s", po::value<int>()->default_value(DEFAULT_SAMPLES), "Monte-Carlo samples used to compute Us")
  		("sphere-file,S", po::value< vector<string> >()->multitoken(), "sphere file:\n [x y z radius material]")
  		("amplitude,a", po::value<ptype>()->default_value(DEFAULT_AMPLITUDE), "incident field amplitude")
  		("n,n", po::value<ptype>()->default_value(DEFAULT_N, "1.4"), "sphere phase speed")
  		("k,k", po::value<ptype>()->default_value(DEFAULT_K), "sphere absorption coefficient")
  		("material-file,M", po::value< vector<string> >()->multitoken(), "material file:\n [lambda n k]")
  		("materials", po::value< vector<ptype> >()->multitoken(), "materials specified using n, k pairs:\n ex. --materials n1 k1 n2 k2\n (if used --n and --k are ignored)")
  		("lambda,l", po::value<ptype>()->default_value(DEFAULT_LAMBDA), "incident wavelength")
  		("theta,t", po::value<ptype>()->default_value(DEFAULT_K_THETA), "light direction (polar coords)")
  		("phi,p", po::value<ptype>()->default_value(DEFAULT_K_PHI))
  		("fx", po::value<ptype>()->default_value(DEFAULT_FOCUS_X), "incident focal point")
  		("fy", po::value<ptype>()->default_value(DEFAULT_FOCUS_Y))
  		("fz", po::value<ptype>()->default_value(DEFAULT_FOCUS_Z))
  		("condenser-max,C", po::value<ptype>()->default_value(DEFAULT_CONDENSER_MAX), "condenser numerical aperature")
  		("condenser-min,c", po::value<ptype>()->default_value(DEFAULT_CONDENSER_MIN), "condenser obscuration NA")
  		("objective-max,O", po::value<ptype>()->default_value(DEFAULT_OBJECTIVE_MAX), "objective numerical aperature")
  		("objective-min,o", po::value<ptype>()->default_value(DEFAULT_OBJECTIVE_MIN), "objective obscuration NA")
  		("field-order", po::value<int>()->default_value(DEFAULT_FIELD_ORDER), "order of the incident field")
  		("output-type,f", po::value<string>()->default_value(DEFAULT_FIELD_TYPE), "output field value:\n magnitude, polarization, real, imaginary, angular-spectrum")
  		("resolution,R", po::value<unsigned int>()->default_value(DEFAULT_SLICE_RES), "resolution of the detector")
  		("padding,d", po::value<unsigned int>()->default_value(DEFAULT_PADDING), "FFT padding for the objective bandpass")
  		("supersample", po::value<unsigned int>()->default_value(DEFAULT_SUPERSAMPLE), "super-sampling rate for the detector field")
  		("colormap", po::value<string>()->default_value(DEFAULT_COLORMAP), "colormap: gray, brewer")
  		("append", "append result to an existing file\n (binary files only)")
  		("plane-min-x,u", po::value<ptype>()->default_value(DEFAULT_SLICE_MIN_X), "lower-left corner of the field slice")
  		("plane-min-y,v", po::value<ptype>()->default_value(DEFAULT_SLICE_MIN_Y))
  		("plane-min-z,w", po::value<ptype>()->default_value(DEFAULT_SLICE_MIN_Z))
  		("plane-max-x,U", po::value<ptype>()->default_value(DEFAULT_SLICE_MAX_X), "upper-right corner of the field slice")
  		("plane-max-y,V", po::value<ptype>()->default_value(DEFAULT_SLICE_MAX_Y))
  		("plane-max-z,W", po::value<ptype>()->default_value(DEFAULT_SLICE_MAX_Z))
  		("plane-norm-x", po::value<ptype>()->default_value(DEFAULT_SLICE_NORM_X), "field slice normal")
  		("plane-norm-y", po::value<ptype>()->default_value(DEFAULT_SLICE_NORM_Y))
  		("plane-norm-z", po::value<ptype>()->default_value(DEFAULT_SLICE_NORM_Z));
  }
  
  static void LoadParameters(int argc, char *argv[])
  {
  	//create an option description
  	po::options_description desc("Allowed options");
  
  	//fill it with options
  	SetOptions(desc);
  
      po::variables_map vm;
  	po::store(po::parse_command_line(argc, argv, desc), vm);
  	po::notify(vm);
  
  	//display help and exit
  	if(vm.count("help"))
  	{
  		cout<<desc<<endl;
  		exit(1);
  	}
  
  	//load spheres
  	loadSpheres(vm);
  
  	//load materials
  	loadMaterials(vm);
  
  	loadNearfieldParams(vm);
  
  	loadOutputParams(vm);
  
  	loadMicroscopeParams(vm);
  
  	loadSliceParams(vm);
  
      //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);
  
      }
  
  
  
  
  
  }