Lemma/Modules/FDEM1D/matlab/hantenna_mex.cpp

/* MyMEXFunction
 * Adds second input to each  
 * element of first input
 * a = MyMEXFunction(a,b);
*/

#include "mex.hpp"
#include "mexAdapter.hpp"
#include "MatlabDataArray.hpp"
#include "LemmaCore"
#include "FDEM1D"
#include "timer.h"
#include <Eigen/Core>

#if defined(__clang__)
	/* Clang/LLVM. ---------------------------------------------- */
    const char* compiler = "clang";
    const char* ver = __VERSION__;
#elif defined(__ICC) || defined(__INTEL_COMPILER)
	/* Intel ICC/ICPC. ------------------------------------------ */
    const char* compiler = "icpc";
    const char* ver = __VERSION__;
#elif defined(__GNUC__) || defined(__GNUG__)
	/* GNU GCC/G++. --------------------------------------------- */
    const char* compiler = "gcc (GCC) ";//  __VERSION__;
    const char* ver = __VERSION__;
#elif defined(_MSC_VER)
	/* Microsoft Visual Studio. --------------------------------- */
    const char* compiler = "msvc ";
    const int ver = _MSC_FULL_VER;
#elif defined(__PGI)
	/* Portland Group PGCC/PGCPP. ------------------------------- */
    const char* compiler = "pgc";
#endif

using namespace Lemma;
using namespace matlab::data;
using matlab::mex::ArgumentList;

std::vector<Real>  readinpfile(const std::string& fname);
std::vector<std::string>  readinpfile2(const std::string& fname);


class MexFunction : public matlab::mex::Function {

public:

    void operator()(ArgumentList outputs, ArgumentList inputs) {
	
	const char *buildString = __DATE__ ", " __TIME__;
    	std::cout
    << "===========================================================================\n"
    << "Lemma " << LEMMA_VERSION << "\n"
    << "[" << compiler << " " << ver << " " <<  buildString << "]\n"
    << "This program is part of Lemma, a geophysical modelling and inversion API. \n"
    << "     This Source Code Form is subject to the terms of the Mozilla Public\n"
    << "     License, v. 2.0. If a copy of the MPL was not distributed with this\n"
    << "     file, You can obtain one at http://mozilla.org/MPL/2.0/. \n"
    << "Copyright (C) 2018 Lemma Software \n"
    << "More information may be found at: https://lemmasoftware.org\n"
    << "                                     info@lemmasoftware.org\n"
    << "===========================================================================\n\n"
    << "Hantenna calculates the harmonic H field from polygonal wire loop sources\n";

	// TODO add this
        //checkArguments(outputs, inputs);
       
        // TODO, add this to check arguments and formalize 	
	if (inputs.size() < 4) {
            std::cout << "usage: hantenna(trans.inp cond.inp points.inp config.inp) \n";
	    ArrayFactory ef;
	    
            outputs[0] = ef.createCharArray("Insufficient inputs");
            return;
	    //exit(EXIT_SUCCESS); 
	}

	#ifdef LEMMAUSEOMP
        std::cout << "OpenMP is using " << omp_get_max_threads() << " threads" << std::endl;
        #endif

	/*
	std::vector<Real> Trans   = readinpfile(std::string(inputs[1]));
        std::vector<Real> CondMod = readinpfile(std::string(inputs[2]));
        std::vector<Real> Points  = readinpfile(std::string(inputs[3]));
        std::vector<std::string> config  = readinpfile2(std::string(inputs[4]));
	*/

	// Let's fix this inputs thing
	matlab::data::CharArray charVector2 = inputs[0];
	std::string TransFile = charVector2.toAscii();

	std::vector<Real> Trans   = readinpfile( "trans.inp" );
        std::vector<std::string> config  = readinpfile2("config.inp");
        std::vector<Real> CondMod = readinpfile("cond.inp");
        std::vector<Real> Points  = readinpfile("points.inp");

	//////////////////////////////////////
        // Define transmitter
        auto trans = PolygonalWireAntenna::NewSP();
            trans->SetNumberOfPoints((int)(Trans[0]));
            int ip=1;
            for ( ; ip<=(int)(Trans[0])*2; ip+=2) {
                trans->SetPoint(ip/2, Vector3r (Trans[ip], Trans[ip+1], -1e-3));
                //trans->SetPoint(ip/2, Vector3r (Trans[ip], Trans[ip+1], 50.));
            }
 	    trans->SetNumberOfFrequencies(1);
 	    trans->SetFrequency(0, Trans[ip]);
            trans->SetCurrent(Trans[ip+1]);
            trans->SetMinDipoleRatio(atof(config[1].c_str()));
            trans->SetMinDipoleMoment(atof(config[2].c_str()));
            trans->SetMaxDipoleMoment(atof(config[3].c_str()));

        /////////////////////////////////////
        // Field calculations
        auto receivers = FieldPoints::NewSP();
            int nx = (int)Points[0];
            int ny = (int)Points[1];
            int nz = (int)Points[2];
            Real ox = Points[3];
            Real oy = Points[4];
            Real oz = Points[5];
     	    Vector3r loc;
            VectorXr dx(nx-1);
            VectorXr dy(ny-1);
            VectorXr dz(nz-1);
            ip = 6;
            int ir = 0;
            for ( ; ip <6+nx-1; ++ip) {
                dx[ir] = Points[ip];
                ++ir;
            }
            ir = 0;
            for ( ; ip <6+ny-1+nx-1; ++ip) {
                dy[ir] = Points[ip];
                ++ir;
            }
            ir = 0;
            for ( ; ip <6+nz-1+ny-1+nx-1; ++ip) {
                dz[ir] = Points[ip];
                ++ir;
            }
            receivers->SetNumberOfPoints(nx*ny*nz);
            ir = 0;
            Real pz  = oz;
            for (int iz=0; iz<nz; ++iz) {
                Real py    =  oy;
                for (int iy=0; iy<ny; ++iy) {
                    Real px    =  ox;
                    for (int ix=0; ix<nx; ++ix) {
                        loc << px, py, pz;
                        receivers->SetLocation(ir, loc);
                        if (ix < nx-1) px += dx[ix];
                        ++ ir;
                    }
                   if (iy<ny-1) py += dy[iy];
                }
                if (iz<nz-1) pz += dz[iz];
            }

	////////////////////////////////////
        // Define model
        auto earth = LayeredEarthEM::NewSP();
            VectorXcr sigma;
            VectorXr  thick;
 	    earth->SetNumberOfLayers(static_cast<int>(CondMod[0])+1);
 	    sigma.resize(static_cast<int>(CondMod[0])+1); sigma(0) = 0; // airlayer
            thick.resize(static_cast<int>(CondMod[0])-1);
            int ilay=1;
            for ( ; ilay/2<CondMod[0]-1; ilay+=2) {
                sigma(ilay/2+1) =  1./CondMod[ilay];
                thick(ilay/2) =  CondMod[ilay+1];
            }
            sigma(ilay/2+1) = 1./ CondMod[ilay];
	    earth->SetLayerConductivity(sigma);
            if (thick.size() > 0) earth->SetLayerThickness(thick);

	auto EmEarth = EMEarth1D::NewSP();
            EmEarth->AttachWireAntenna(trans);
            EmEarth->AttachLayeredEarthEM(earth);
            EmEarth->AttachFieldPoints(receivers);
            EmEarth->SetFieldsToCalculate(H);
            EmEarth->SetHankelTransformMethod(string2Enum<HANKELTRANSFORMTYPE>(config[0]));

        ///////////////////////////////////////////////
        // Keep track of time
	jsw_timer timer;
  	timer.begin();
        clock_t launch = clock();
        EmEarth->CalculateWireAntennaFields(false);    // false=status bar, doesn't work in Matlab well 
        Real paTime = timer.end();

        std::cout << "\n\n===========================================\ncalc. real time: " << paTime/60. << "\t[m]\n";
        std::cout << "calc. user time: " <<  (clock()-launch)/CLOCKS_PER_SEC/60.   << "\t[CPU m]"
                  << std::endl;


	////////////////////////////////////////////////////////////////////
	// This is kind of ugly, but the Matlab conversion is really picky
	// Convert C++ arrays to Matlab 
        
	ArrayFactory f;
	StructArray S = f.createStructArray({ 3,1 }, { "Component", "Data", "Units" });
	
	S[0]["Component"] = f.createCharArray("H_x");
	S[0]["Units"] = f.createCharArray("A/m");
	Eigen::Array<Complex, Eigen::Dynamic, 1> Hx = receivers->GetHfield(0).row(0).array(); 
	std::vector<Complex> Hxv = std::vector<Complex>(Hx.begin(), Hx.end());
	matlab::data::TypedArray<Complex> Hxm = f.createArray<Complex>({1, Hxv.size()}, Hxv.data(), Hxv.data()+Hxv.size());
	S[0]["Data"] = std::move(Hxm);

        S[1]["Component"] = f.createCharArray("H_y");
	S[1]["Units"] = f.createCharArray("A/m");
	Eigen::Array<Complex, Eigen::Dynamic, 1> Hy = receivers->GetHfield(0).row(1).array(); 
	std::vector<Complex> Hyv = std::vector<Complex>(Hy.begin(), Hy.end());
	matlab::data::TypedArray<Complex> Hym = f.createArray<Complex>({1, Hyv.size()}, Hyv.data(), Hyv.data()+Hyv.size());
	S[1]["Data"] = std::move(Hym);
        
	S[2]["Component"] = f.createCharArray("H_z");
	S[2]["Units"] = f.createCharArray("A/m");
	Eigen::Array<Complex, Eigen::Dynamic, 1> Hz = receivers->GetHfield(0).row(2).array(); 
	std::vector<Complex> Hzv = std::vector<Complex>(Hz.begin(), Hz.end());
	matlab::data::TypedArray<Complex> Hzm = f.createArray<Complex>({1, Hzv.size()}, Hzv.data(), Hzv.data()+Hzv.size());
	S[2]["Data"] = std::move(Hzm);
	

	outputs[0] = std::move(S);

	////////////////////////////////////
        // Report, file write is s l o w 
	/*
        std::fstream hrep("hfield.yaml", std::ios::out);
        std::fstream hreal("hfield.dat", std::ios::out);

        hrep << *EmEarth << std::endl;
        hrep.close();

        hreal << "// Right hand coordinate system, z is positive down\n";
        hreal << "// x[m]\ty[m]\tz[m]\tRe(Hx[A/m])\tRe(Hy[A/m])\tRe(Hz[A/m])\tIm(Hx)\tIm(Hy)\tIm(Hz)\n";
        hreal.precision(8);
        int i=0;
	for (int iz=0; iz<nz; ++iz) {
	for (int iy=0; iy<ny; ++iy) {
	for (int ix=0; ix<nx; ++ix) {
            hreal << receivers->GetLocation(i).transpose() << "\t";
 		hreal << receivers->GetHfield(0, i).transpose() << "\n"; // ( complex, notation )
 		//hreal << receivers->GetHfield(0, i).transpose().real() << "\t";
 		//hreal << receivers->GetHfield(0, i).transpose().imag() << "\n";
            ++i;
        }
        }
        }
        hreal.close();
        */ 

        // Demo stuff
	/*
	const double offSet = inputs[0][0];
	TypedArray<double> doubleArray = std::move(inputs[1]);
        for (auto& elem : doubleArray) {
            elem += offSet;
        }
	outputs[0] = doubleArray;
	*/
    }

    void checkArguments(ArgumentList outputs, ArgumentList inputs) {

        // Get pointer to engine
        std::shared_ptr<matlab::engine::MATLABEngine> matlabPtr = getEngine();

        // Get array factory
        ArrayFactory factory;

        // Check first input argument
        if (inputs[0].getType() != ArrayType::CHAR ||
            inputs[0].getNumberOfElements() != 1)
        {
            matlabPtr->feval(u"error",
                0,
                std::vector<Array>({ factory.createScalar("First input must be the name of a trans.inp file") }));
        }

        // Check second input argument
        if (inputs[1].getType() != ArrayType::DOUBLE ||
            inputs[1].getType() == ArrayType::COMPLEX_DOUBLE)
        {
            matlabPtr->feval(u"error",
                0,
                std::vector<Array>({ factory.createScalar("Input must be double array") }));
        }
        // Check number of outputs
        if (outputs.size() > 1) {
            matlabPtr->feval(u"error",
                0,
                std::vector<Array>({ factory.createScalar("Only one output is returned") }));
        }
    }
};

std::vector<Real>  readinpfile(const std::string& fname) {
    std::string buf;
    char dump[255];
    std::vector<Real> vals;
    std::fstream input(fname.c_str(), std::ios::in);
    if (input.fail()) {
        std::cerr << "Input file " << fname << " failed to open\n";
        exit(EXIT_FAILURE);
    }
    while (input >> buf) {
        if (buf.substr(0,2) == "//") {
            input.getline(dump, 255);
        } else {
            vals.push_back( atof(buf.c_str() ));
        }
    }
    return vals;
}

std::vector<std::string>  readinpfile2(const std::string& fname) {
    std::string buf;
    char dump[255];
    std::vector<std::string> vals;
    std::fstream input(fname.c_str(), std::ios::in);
    if (input.fail()) {
        std::cerr << "Input file " << fname << " failed to open\n";
        exit(EXIT_FAILURE);
    }
    while (input >> buf) {
        if (buf.substr(0,2) == "//") {
            input.getline(dump, 255);
        } else {
            vals.push_back( std::string(buf.c_str() ));
        }
    }
    return vals;
}