ophSigCH.cpp

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#include "ophSigCH.h"

ophSigCH::ophSigCH(void) 
    : Nz(0)
    , MaxIter(0)
    , Tau(0)
    , TolA(0)
    , TvIter(0)
{
}

bool ophSigCH::saveNumRec(const char *fname)
{
    double gamma = 0.5;

    oph::uchar* intensityData;
    intensityData = (oph::uchar*)malloc(sizeof(oph::uchar) * _cfgSig.rows * _cfgSig.cols);
    double maxIntensity = 0.0;
    double realVal = 0.0;
    double imagVal = 0.0;
    double intensityVal = 0.0;
    for (int k = 0; k < Nz; k++)
    {
        for (int i = 0; i < _cfgSig.rows; i++)
        {
            for (int j = 0; j < _cfgSig.cols; j++)
            {
                realVal = NumRecRealImag(i, j + k*_cfgSig.cols);
                imagVal = NumRecRealImag(i + _cfgSig.rows, j + k*_cfgSig.cols);
                intensityVal = realVal*realVal + imagVal*imagVal;
                if (intensityVal > maxIntensity)
                {
                    maxIntensity = intensityVal;
                }
            }
        }
    }

    string fnamestr = fname;
    int checktype = static_cast<int>(fnamestr.rfind("."));
    char str[10];

    for (int k = 0; k < Nz; k++)
    {
        fnamestr = fname;
        for (int i = _cfgSig.rows - 1; i >= 0; i--)
        {
            for (int j = 0; j < _cfgSig.cols; j++)
            {
                realVal = NumRecRealImag(i, j + k*_cfgSig.cols);
                imagVal = NumRecRealImag(i + _cfgSig.rows, j + k*_cfgSig.cols);
                intensityVal = realVal*realVal + imagVal*imagVal;
                intensityData[i*_cfgSig.cols + j] = (uchar)(pow(intensityVal / maxIntensity,gamma)*255.0);
            }
        }
        sprintf(str, "_%.2d", k);
        fnamestr.insert(checktype, str);
        saveAsImg(fnamestr.c_str(), 8, intensityData, _cfgSig.cols, _cfgSig.rows);
    }

    return true;
}

bool ophSigCH::setCHparam(vector<Real> &z, int maxIter, double tau, double tolA, int tvIter) {
    MaxIter = maxIter;
    Tau = tau;
    TolA = tolA;
    TvIter = tvIter;
    Z.resize(z.size());
    Z = z;
    Nz = Z.size();
    return true;
}

bool ophSigCH::runCH(int complexHidx) 
{
    auto start_time = CUR_TIME;

    matrix<Real> realimagplaneinput(_cfgSig.rows*2, _cfgSig.cols);
    c2ri(ComplexH[complexHidx], realimagplaneinput);

    NumRecRealImag.resize(_cfgSig.rows * 2, _cfgSig.cols*Nz);   
    twist(realimagplaneinput, NumRecRealImag);

    auto end_time = CUR_TIME;

    auto during_time = ((std::chrono::duration<Real>)(end_time - start_time)).count();

    LOG("Implement time : %.5lf sec\n", during_time);

    return true;
}

void ophSigCH::tvdenoise(matrix<Real>& input, double lam, int iters, matrix<Real>& output)
{
    double dt = 0.25;
    int nr = input.size(_X);
    int nc = input.size(_Y);
    matrix<Real> divp(nr, nc);
    divp.zeros();
        
    matrix<Real> z(nr, nc);
    matrix<Real> z1, z2;
    z1.resize(nr, nc);
    z2.resize(nr, nc);

    matrix<Real> p1, p2;
    p1.resize(nr, nc);
    p2.resize(nr, nc);

    matrix<Real> denom(nr, nc);

    for (int iter = 0; iter < iters; iter++)
    {
        for (int i = 0; i < nr; i++)
        {
            for (int j = 0; j < nc; j++)
            {
                z(i,j) = divp(i, j) - input(i, j)*lam;
            }
        }

        for (int i = 0; i < nr - 1; i++)
        {
            for (int j = 0; j < nc - 1; j++)
            {
                z1(i, j) = z(i, j + 1) - z(i, j);
                z2(i, j) = z(i + 1, j) - z(i, j);
                denom(i, j) = 1 + dt*sqrt(z1(i, j)*z1(i, j) + z2(i, j)*z2(i, j));
            }
        }
        for (int i = 0; i < nr-1; i++)
        {
            z1(i, nc-1) = 0.0;
            z2(i, nc-1) = z(i + 1, nc-1) - z(i, nc-1);
            denom(i, nc-1) = 1 + dt*sqrt(z1(i, nc-1)*z1(i, nc-1) + z2(i, nc-1)*z2(i, nc-1));
        }
        for (int j = 0; j < nc - 1; j++)
        {
            z1(nr-1, j) = z(nr-1, j+1) - z(nr-1, j);
            z2(nr-1, j) = 0.0;
            denom(nr-1, j) = 1 + dt*sqrt(z1(nr-1, j)*z1(nr-1, j) + z2(nr-1, j)*z2(nr-1, j));
        }
        denom(nr-1, nc-1) = 1.0;
        z1(nr - 1, nc - 1) = 0.0;
        z2(nr - 1, nc - 1) = 0.0;


        for (int i = 0; i < nr ; i++)
        {
            for (int j = 0; j < nc; j++)
            {
                p1(i, j) = (p1(i, j) + dt*z1(i, j)) / denom(i, j);
                p2(i, j) = (p2(i, j) + dt*z2(i, j)) / denom(i, j);
            }
        }

        for (int i = 1; i < nr; i++)
        {
            for (int j = 1; j < nc; j++)
            {
                divp(i, j) = p1(i, j) - p1(i, j - 1) + p2(i, j) - p2(i - 1, j);
            }
        }
        for (int i = 1; i < nr; i++)
        {
            divp(i, 0) = p2(i, 0) - p2(i-1, 0);
        }
        for (int j = 1; j < nc; j++)
        {
            divp(0, j) = p1(0, j) - p1(0, j - 1);
        }
        divp(0, 0) = 0.0;

    }

    for (int i = 0; i < input.size[_X]; i++)
    {
        for (int j = 0; j < input.size[_Y]; j++)
        {
            output(i, j) = input(i,j) - divp(i, j)/lam;
        }
    }

}

double ophSigCH::tvnorm(matrix<Real>& input)
{
    double sqrtsum = 0.0;
    int nr = input.size[_X];
    int nc = input.size[_Y];

    for (int i = 0; i < nr-1; i++)
    {
        for (int j = 0; j < nc-1; j++)
        {
            sqrtsum += sqrt((input(i,j)-input(i+1,j))*(input(i,j)-input(i+1,j)) + (input(i,j)-input(i,j+1))*(input(i,j)-input(i,j+1)));
        }
    }
    for (int i = 0; i < nr-1; i++)
    {
        sqrtsum += sqrt(pow(input(i, nc-1) - input(i + 1, nc-1), 2) + pow(input(i, nc-1) - input(i, 0), 2));
    }
    for (int j = 0; j < nc - 1; j++)
    {
        sqrtsum += sqrt(pow(input(nr-1, j) - input(0, j), 2) + pow(input(nr-1, j) - input(nr-1, j+1), 2));
    }
    sqrtsum += sqrt(pow(input(nr-1, nc-1) - input(0, nc-1), 2) + pow(input(nr-1, nc-1) - input(nr-1, 0), 2));

    return sqrtsum;
}

void ophSigCH::c2ri(matrix<Complex<Real>>& complexinput, matrix<Real>& realimagoutput)
{
    for (int i = 0; i < complexinput.size[_X]; i++)
    {
        for (int j = 0; j < complexinput.size[_Y]; j++)
        {
            realimagoutput(i, j) = complexinput(i, j)[_RE];
            realimagoutput(i + complexinput.size[_X], j) = complexinput(i, j)[_IM];
        }
    }
    
}

void ophSigCH::ri2c(matrix<Real>& realimaginput, matrix<Complex<Real>>& complexoutput)
{
    for (int i = 0; i < complexoutput.size[_X]; i++)
    {
        for (int j = 0; j < complexoutput.size[_Y]; j++)
        {
            complexoutput(i, j)[_RE] = realimaginput(i, j);
            complexoutput(i, j)[_IM] = realimaginput(i + complexoutput.size[_X], j);
        }
    }
}

void ophSigCH::volume2plane(matrix<Real>& realimagvolumeinput, vector<Real> z, matrix<Real>& realimagplaneoutput)
{
    int nz = z.size();
    int nr = realimagvolumeinput.size(_X) >> 1; // real imag
    int nc = realimagvolumeinput.size(_Y) / nz;

    matrix<Complex<Real>> complexTemp(nr,nc);
    matrix<Complex<Real>> complexAccum(nr, nc);
    complexAccum.zeros();

    for (int k = 0; k < nz; k++)
    {
        int temp = k * nc;
        for (int i = 0; i < nr; i++)
        {
            for (int j = 0; j < nc; j++)
            {
                complexTemp(i, j)[_RE] = realimagvolumeinput(i, j + temp);
                complexTemp(i, j)[_IM] = realimagvolumeinput(i + nr, j + temp);
            }
        }
        OphComplexField result = propagationHoloAS(complexTemp, static_cast<float>(z.at(k)));
        complexAccum = complexAccum + result;
    }
    c2ri(complexAccum, realimagplaneoutput);
}


void ophSigCH::plane2volume(matrix<Real>& realimagplaneinput, vector<Real> z, matrix<Real>& realimagplaneoutput)
{
    int nr = realimagplaneinput.size(_X)/2;
    int nc = realimagplaneinput.size(_Y);
    int nz = z.size();

    matrix<Complex<Real>> complexplaneinput(nr, nc);
    for (int i = 0; i < nr; i++)
    {
        for (int j = 0; j < nc; j++)
        {
            complexplaneinput(i, j)[_RE] = realimagplaneinput(i, j);
            complexplaneinput(i, j)[_IM] = realimagplaneinput(i + nr, j);
        }
    }


    matrix<Complex<Real>> temp(nr, nc);
    for (int k = 0; k < nz; k++)
    {
        temp = propagationHoloAS(complexplaneinput, static_cast<float>(-z.at(k)));
        for (int i = 0; i < nr; i++)
        {
            for (int j = 0; j < nc; j++)
            {
                realimagplaneoutput(i, j + k*nc) = temp(i, j)[_RE];
                realimagplaneoutput(i + nr, j + k*nc) = temp(i, j)[_IM];
            }
        }
    }

}

void ophSigCH::convert3Dto2D(matrix<Complex<Real>>* complex3Dinput, int nz, matrix<Complex<Real>>& complex2Doutput)
{
    int nr = complex3Dinput[0].size(_X);
    int nc = complex3Dinput[0].size(_Y);

    for (int i = 0; i < nr; i++)
    {
        for (int j = 0; j < nc; j++)
        {
            for (int k = 0; k < nz; k++)
            {
                complex2Doutput(i, j + k*nc) = complex3Dinput[k](i, j);
            }
        }
    }
}

void ophSigCH::convert2Dto3D(matrix<Complex<Real>>& complex2Dinput, int nz, matrix<Complex<Real>>* complex3Doutput)
{
    int nr = complex2Dinput.size(_X);
    int nc = complex2Dinput.size(_Y)/nz;

    for (int k = 0; k < nz; k++)
    {
        for (int i = 0; i < nr; i++)
        {
            for (int j = 0; j < nc; j++)
            {
                complex3Doutput[k](i, j) = complex2Dinput(i, j + k*nc);
            }
        }
    }
}

void ophSigCH::twist(matrix<Real>& realimagplaneinput, matrix<Real>& realimagvolumeoutput)
{
    //
    int nrv = realimagvolumeoutput.size(_X);
    int ncv = realimagvolumeoutput.size(_Y);
    int nrp = realimagplaneinput.size(_X);
    int ncp = realimagplaneinput.size(_Y);


    // TWiST
    double stopCriterion = 1;
    double tolA = TolA;
    int maxiter = MaxIter;
    int miniter = MaxIter;
    int init = 2;
    bool enforceMonotone = 1;
    bool compute_mse = 0;
    bool plot_ISNR = 0;
    bool verbose = 1;
    double alpha = 0;
    double beta = 0;
    bool sparse = 1;
    double tolD = 0.001;
    double phi_l1 = 0;
    double psi_ok = 0;
    double lam1 = 1e-4;
    double lamN = 1;
    double tau = Tau;
    int tv_iters = TvIter;

    bool for_ever = 1;
    double max_svd = 1;

    // twist parameters
    double rho0 = (1. - lam1 / lamN) / (1. + lam1 / lamN);
    if (alpha == 0) {
        alpha = 2. / (1 + sqrt(1 - pow(rho0, 2)));
    }
    if (beta == 0) {
        beta = alpha*2. / (lam1 + lamN);
    }

    double prev_f = 0.0;
    double f = 0.0;

    double criterion = 0.0;

    // initialization
    plane2volume(realimagplaneinput, Z, realimagvolumeoutput);

    // compute and sotre initial value of the objective function
    matrix<Real> resid(nrp, ncp);
    volume2plane(realimagvolumeoutput, Z, resid);
    for (int i = 0; i < nrp; i++)
    {
        for (int j = 0; j < ncp; j++)
        {
            resid(i, j) = realimagplaneinput(i, j) - resid(i, j);
        }
    }
    prev_f = 0.5*matrixEleSquareSum(resid) + tau*tvnorm(realimagvolumeoutput);

    //
    int iter = 0;
    bool cont_outer = 1;

    if (verbose)
    {
        LOG("initial objective = %10.6e\n", prev_f);
    }

    int IST_iters = 0;
    int TwIST_iters = 0;

    // initialize
    matrix<Real> xm1, xm2;
    xm1.resize(nrv, ncv);
    xm2.resize(nrv, ncv);
    xm1 = realimagvolumeoutput;
    xm2 = realimagvolumeoutput;

    // TwIST iterations
    matrix<Real> grad, temp_volume;
    grad.resize(nrv, ncv);
    temp_volume.resize(nrv, ncv);
    while (cont_outer)
    {
        plane2volume(resid, Z, grad);
        while (for_ever)
        {
            for (int i = 0; i < nrv; i++)
            {
                for (int j = 0; j < ncv; j++)
                {
                    temp_volume(i, j) = xm1(i, j) + grad(i, j) / max_svd;
                }
            }
            tvdenoise(temp_volume, 2.0 / (tau / max_svd), tv_iters, realimagvolumeoutput);
            
            if ((IST_iters >= 2) | (TwIST_iters != 0))
            {
                if (sparse)
                {
                    for (int i = 0; i < nrv; i++)
                    {
                        for (int j = 0; j < ncv; j++)
                        {
                            if (realimagvolumeoutput(i, j) == 0)
                            {
                                xm1(i, j) = 0.0;
                                xm2(i, j) = 0.0;
                            }
                        }
                    }
                        
                }
                // two step iteration
                for (int i = 0; i < nrv; i++)
                {
                    for (int j = 0; j < ncv; j++)
                    {
                        xm2(i, j) = (alpha - beta)*xm1(i, j) + (1.0 - alpha)*xm2(i, j) + beta*realimagvolumeoutput(i, j);
                    }
                }
                // compute residual
                volume2plane(xm2, Z, resid);
                
                for (int i = 0; i < nrp; i++)
                {
                    for (int j = 0; j < ncp; j++)
                    {
                        resid(i, j) = realimagplaneinput(i, j) - resid(i, j);
                    }
                }
                f = 0.5*matrixEleSquareSum(resid) + tau*tvnorm(xm2);
                if ((f > prev_f) & (enforceMonotone))
                {
                    TwIST_iters = 0;
                }
                else
                {
                    TwIST_iters += 1;
                    IST_iters = 0;
                    realimagvolumeoutput = xm2;
                    if (TwIST_iters % 10000 == 0)
                    {
                        max_svd = 0.9*max_svd;
                    }
                    break;
                }
            }
            else
            {
                volume2plane(realimagvolumeoutput, Z, resid);
                for (int i = 0; i < nrp; i++)
                {
                    for (int j = 0; j < ncp; j++)
                    {
                        resid(i, j) = realimagplaneinput(i, j) - resid(i, j);
                    }
                }
                f = 0.5*matrixEleSquareSum(resid) + tau*tvnorm(realimagvolumeoutput);
                if (f > prev_f)
                {
                    max_svd = 2 * max_svd;
                    if (verbose)
                    {
                        LOG("Incrementing S = %2.2e\n", max_svd);
                    }
                    IST_iters = 0;
                    TwIST_iters = 0;
                }
                else
                {
                    TwIST_iters += 1;
                    break;
                }
            }

        }
        xm2 = xm1;
        xm1 = realimagvolumeoutput;

        criterion = (abs(f - prev_f)) / prev_f;

        cont_outer = ((iter <= maxiter) & (criterion > tolA));
        if (iter <= miniter)
        {
            cont_outer = 1;
        }

        iter += 1;
        prev_f = f;

        if (verbose)
        {
            LOG("Iteration=%4d, objective=%9.5e, criterion=%7.3e\n", iter, f, criterion / tolA);
        }
    }

    if (verbose)
    {
        double sum_abs_x=0.0;
        for (int i = 0; i < nrv; i++)
        {
            for (int j = 0; j < ncv; j++)
            {
                sum_abs_x += abs(realimagvolumeoutput(i, j));
            }
        }
        LOG("\n Finishied the main algorithm!\n");
        LOG("||Ax-y||_2 = %10.3e\n", matrixEleSquareSum(resid));
        LOG("||x||_1 = %10.3e\n", sum_abs_x);
        LOG("Objective function = %10.3e\n", f);
    }
}

double ophSigCH::matrixEleSquareSum(matrix<Real>& input)
{
    double output = 0.0;
    for (int i = 0; i < input.size(_X); i++)
    {
        for (int j = 0; j < input.size(_Y); j++)
        {
            output += input(i, j)*input(i, j);
        }
    }
    return output;
}

bool ophSigCH::readConfig(const char* fname)
{
    LOG("CH Reading....%s...\n", fname);

    /*XML parsing*/
    tinyxml2::XMLDocument xml_doc;
    tinyxml2::XMLNode *xml_node;

    if (!checkExtension(fname, ".xml"))
    {
        LOG("file's extension is not 'xml'\n");
        return false;
    }
    auto ret = xml_doc.LoadFile(fname);
    if (ret != tinyxml2::XML_SUCCESS)
    {
        LOG("Failed to load file \"%s\"\n", fname);
        return false;
    }

    xml_node = xml_doc.FirstChild();

    (xml_node->FirstChildElement("rows"))->QueryIntText(&_cfgSig.rows);
    (xml_node->FirstChildElement("cols"))->QueryIntText(&_cfgSig.cols);
    (xml_node->FirstChildElement("width"))->QueryFloatText(&_cfgSig.width);
    (xml_node->FirstChildElement("height"))->QueryFloatText(&_cfgSig.height);
    (xml_node->FirstChildElement("wavelength"))->QueryDoubleText(&_cfgSig.wavelength[0]);
    (xml_node->FirstChildElement("nz"))->QueryIntText(&Nz);
    (xml_node->FirstChildElement("maxiter"))->QueryIntText(&MaxIter);
    (xml_node->FirstChildElement("tau"))->QueryDoubleText(&Tau);
    (xml_node->FirstChildElement("tolA"))->QueryDoubleText(&TolA);
    (xml_node->FirstChildElement("tv_iters"))->QueryIntText(&TvIter);

    double zmin, dz;
    (xml_node->FirstChildElement("zmin"))->QueryDoubleText(&zmin);
    (xml_node->FirstChildElement("dz"))->QueryDoubleText(&dz);
    
    Z.resize(Nz);
    for (int i = 0; i < Nz; i++)
    {
        Z.at(i) = zmin + i*dz;
    }
    
    return true;
}

bool ophSigCH::loadCHtemp(const char * real, const char * imag, uint8_t bitpixel)
{
    string realname = real;
    string imagname = imag;
    int checktype = static_cast<int>(realname.rfind("."));
    matrix<Real> realMat[3], imagMat[3];

    std::string realtype = realname.substr(checktype + 1, realname.size());
    std::string imgtype = imagname.substr(checktype + 1, realname.size());
    size_t nRead;

    if (realtype != imgtype) {
        LOG("failed : The data type between real and imaginary is different!\n");
        return false;
    }
    if (realtype == "bmp")
    {
        FILE* freal = nullptr;
        FILE* fimag = nullptr;
        fileheader hf;
        bitmapinfoheader hInfo;
        freal = fopen(realname.c_str(), "rb");
        fimag = fopen(imagname.c_str(), "rb");
        if (freal == nullptr)
        {
            LOG("real bmp file open fail!\n");
            return false;
        }
        if (fimag == nullptr)
        {
            LOG("imaginary bmp file open fail!\n");
            return false;
        }
        nRead = fread(&hf, sizeof(fileheader), 1, freal);
        nRead = fread(&hInfo, sizeof(bitmapinfoheader), 1, freal);
        nRead = fread(&hf, sizeof(fileheader), 1, fimag);
        nRead = fread(&hInfo, sizeof(bitmapinfoheader), 1, fimag);

        if (hf.signature[0] != 'B' || hf.signature[1] != 'M') { LOG("Not BMP File!\n"); }
        if ((hInfo.height == 0) || (hInfo.width == 0))
        {
            LOG("bmp header is empty!\n");
            hInfo.height = _cfgSig.rows;
            hInfo.width = _cfgSig.cols;
            if (_cfgSig.rows == 0 || _cfgSig.cols == 0)
            {
                LOG("check your parameter file!\n");
                return false;
            }
        }
        if ((_cfgSig.rows != (int)hInfo.height) || (_cfgSig.cols != (int)hInfo.width)) {
            LOG("image size is different!\n");
            _cfgSig.rows = hInfo.height;
            _cfgSig.cols = hInfo.width;
            LOG("changed parameter of size %d x %d\n", _cfgSig.cols, _cfgSig.rows);
        }
        hInfo.bitsperpixel = bitpixel;
        if (bitpixel == 8)
        {
            rgbquad palette[256];
            ComplexH = new OphComplexField;
            nRead = fread(palette, sizeof(rgbquad), 256, freal);
            nRead = fread(palette, sizeof(rgbquad), 256, fimag);

            realMat[0].resize(hInfo.height, hInfo.width);
            imagMat[0].resize(hInfo.height, hInfo.width);
            ComplexH[0].resize(hInfo.height, hInfo.width);
        }
        else
        {
            ComplexH = new OphComplexField[3];
            realMat[0].resize(hInfo.height, hInfo.width);
            imagMat[0].resize(hInfo.height, hInfo.width);
            ComplexH[0].resize(hInfo.height, hInfo.width);

            realMat[1].resize(hInfo.height, hInfo.width);
            imagMat[1].resize(hInfo.height, hInfo.width);
            ComplexH[1].resize(hInfo.height, hInfo.width);

            realMat[2].resize(hInfo.height, hInfo.width);
            imagMat[2].resize(hInfo.height, hInfo.width);
            ComplexH[2].resize(hInfo.height, hInfo.width);
        }
        size_t size = hInfo.width * hInfo.height * (hInfo.bitsperpixel >> 3);
        uchar* realdata = (uchar*)malloc(sizeof(uchar) * size);
        uchar* imagdata = (uchar*)malloc(sizeof(uchar) * size);
        nRead = fread(realdata, sizeof(uchar), size, freal);
        nRead = fread(imagdata, sizeof(uchar), size, fimag);

        fclose(freal);
        fclose(fimag);

        for (int i = hInfo.height - 1; i >= 0; i--)
        {
            for (int j = 0; j < static_cast<int>(hInfo.width); j++)
            {
                for (int z = 0; z < (hInfo.bitsperpixel / 8); z++)
                {
                    realMat[z](hInfo.height - i - 1, j) = (double)realdata[i*hInfo.width*(hInfo.bitsperpixel / 8) + (hInfo.bitsperpixel / 8)*j + z];
                    imagMat[z](hInfo.height - i - 1, j) = (double)imagdata[i*hInfo.width*(hInfo.bitsperpixel / 8) + (hInfo.bitsperpixel / 8)*j + z];
                }
            }
        }
        LOG("file load complete!\n");

        free(realdata);
        free(imagdata);
    }
    else if (realtype == "bin")
    {
        if (bitpixel == 8)
        {

            ifstream freal(realname, ifstream::binary);
            ifstream fimag(imagname, ifstream::binary);
            realMat[0].resize(_cfgSig.rows, _cfgSig.cols); imagMat[0].resize(_cfgSig.rows, _cfgSig.cols);
            ComplexH[0].resize(_cfgSig.rows, _cfgSig.cols);
            int total = _cfgSig.rows*_cfgSig.cols;
            double *realdata = new double[total];
            double *imagdata = new double[total];
            int i = 0;
            freal.read(reinterpret_cast<char*>(realdata), sizeof(double) * total);
            fimag.read(reinterpret_cast<char*>(imagdata), sizeof(double) * total);

            for (int col = 0; col < _cfgSig.cols; col++)
            {
                for (int row = 0; row < _cfgSig.rows; row++)
                {
                    realMat[0](row, col) = realdata[_cfgSig.rows*col + row];
                    imagMat[0](row, col) = imagdata[_cfgSig.rows*col + row];
                }
            }

            freal.close();
            fimag.close();
            delete[]realdata;
            delete[]imagdata;
        }
        else if (bitpixel == 24)
        {
            realMat[0].resize(_cfgSig.rows, _cfgSig.cols);
            imagMat[0].resize(_cfgSig.rows, _cfgSig.cols);
            ComplexH[0].resize(_cfgSig.rows, _cfgSig.cols);

            realMat[1].resize(_cfgSig.rows, _cfgSig.cols);
            imagMat[1].resize(_cfgSig.rows, _cfgSig.cols);
            ComplexH[1].resize(_cfgSig.rows, _cfgSig.cols);

            realMat[2].resize(_cfgSig.rows, _cfgSig.cols);
            imagMat[2].resize(_cfgSig.rows, _cfgSig.cols);
            ComplexH[2].resize(_cfgSig.rows, _cfgSig.cols);

            int total = _cfgSig.rows*_cfgSig.cols;


            string RGB_name[] = { "_B","_G","_R" };
            double *realdata = new  double[total];
            double *imagdata = new  double[total];
            char* context = nullptr;

            for (int z = 0; z < (bitpixel / 8); z++)
            {
                ifstream freal(strtok((char*)realname.c_str(), ".") + RGB_name[z] + "bin", ifstream::binary);
                ifstream fimag(strtok((char*)imagname.c_str(), ".") + RGB_name[z] + "bin", ifstream::binary);

                freal.read(reinterpret_cast<char*>(realdata), sizeof(double) * total);
                fimag.read(reinterpret_cast<char*>(imagdata), sizeof(double) * total);

                for (int col = 0; col < _cfgSig.cols; col++)
                {
                    for (int row = 0; row < _cfgSig.rows; row++)
                    {
                        realMat[z](row, col) = realdata[_cfgSig.rows*col + row];
                        imagMat[z](row, col) = imagdata[_cfgSig.rows*col + row];
                    }
                }
                freal.close();
                fimag.close();
            }
            delete[] realdata;
            delete[] imagdata;
        }
    }
    else
    {
        LOG("wrong type\n");
    }

    //nomalization 
    //double realout, imagout;
    for (int z = 0; z < (bitpixel) / 8; z++)
    {
        for (int i = 0; i < _cfgSig.rows; i++)
        {
            for (int j = 0; j < _cfgSig.cols; j++)
            {
                ComplexH[z](i, j)[_RE] = realMat[z](i, j)/255.0*2.0-1.0;
                ComplexH[z](i, j)[_IM] = imagMat[z](i, j)/255.0*2.0-1.0;

            }
        }
    }
    LOG("data nomalization complete\n");

    return true;
}

matrix<Complex<Real>> ophSigCH::propagationHoloAS(matrix<Complex<Real>> complexH, float depth) {
    int nr = _cfgSig.rows;
    int nc = _cfgSig.cols;
    
    double dr = _cfgSig.height / _cfgSig.rows;
    double dc = _cfgSig.width / _cfgSig.cols;

    int nr2 = 2 * nr;
    int nc2 = 2 * nc;

    oph::matrix<oph::Complex<Real>> src2(nr2,nc2);  // prepare complex matrix with 2x size (to prevent artifacts caused by circular convolution)
    src2 * 0;   // initialize to 0

    int iStart = nr / 2 - 1;
    int jStart = nc / 2 - 1;
    for (int i = 0; i < nr; i++)
    {
        for (int j = 0; j < nc; j++)
        {
            src2(i+iStart, j+jStart)[_RE] = complexH(i, j)[_RE];
            src2(i+iStart, j+jStart)[_IM] = complexH(i, j)[_IM];

        }
    }

    double dfr = 1.0 / (((double)nr2)*dr);  // spatial frequency step in src2
    double dfc = 1.0 / (((double)nc2)*dc);

    matrix<Complex<Real>> propKernel(nr2, nc2);
    double fz = 0;
    for (int i = 0; i < nr2; i++)
    {
        for (int j = 0; j < nc2; j++)
        {
            fz = sqrt(pow(1.0 / _cfgSig.wavelength[0], 2) - pow((i - nr2 / 2.0 + 1.0)*dfr, 2) - pow((j - nc2 / 2.0 + 1.0)*dfc, 2));
            propKernel(i, j)[_RE] = cos(2 * M_PI*depth*fz);
            propKernel(i, j)[_IM] = sin(2 * M_PI*depth*fz);
        }
    }

    matrix<Complex<Real>> src2temp(nr2, nc2);
    matrix<Complex<Real>> FFZP(nr2, nc2);
    matrix<Complex<Real>> FFZP2(nr2, nc2);
    fftShift(src2, src2temp);
    fft2(src2temp, FFZP, OPH_FORWARD);
    fftShift(FFZP, FFZP2);
    FFZP2.mulElem(propKernel);

    fftShift(FFZP2, FFZP);
    fft2(FFZP, src2temp, OPH_BACKWARD);
    fftShift(src2temp, src2);

    matrix<Complex<Real>> dst(nr, nc);
    for (int i = 0; i < nr; i++)
    {
        for (int j = 0; j < nc; j++)
        {
            dst(i,j)[_RE] = src2(i + iStart , j + jStart)[_RE];
            dst(i,j)[_IM] = src2(i + iStart , j + jStart)[_IM];
        }
    }
    return dst;
}