ophRec.cpp

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#include "ophRec.h"
#include "sys.h"
#include "function.h"
#include "tinyxml2.h"
#include "ImgControl.h"
#include <algorithm>
//#include "fftw3.h"
#include <omp.h>

ophRec::ophRec(void)
    : Openholo()
    , m_oldSimStep(0)
    , m_nOldChannel(0)
    , m_idx(0)
{
}

ophRec::~ophRec(void)
{
}
#define IMAGE_VAL(x,y,c,w,n,mem) (mem[x*n + y*w*n + c])
vec3 image_sample(float xx, float yy, int c, size_t w, size_t h, double* in);
void circshift(Real* in, Real* out, int shift_x, int shift_y, int nx, int ny);
void circshift(Complex<Real>* in, Complex<Real>* out, int shift_x, int shift_y, int nx, int ny);
void ScaleBilnear(double* src, double* dst, int w, int h, int neww, int newh, double multiplyval = 1.0);
void reArrangeChannel(std::vector<double*>& src, double* dst, int pnx, int pny, int chnum);
void rotateCCW180(double* src, double* dst, int pnx, int pny, double mulival = 1.0);

bool ophRec::readConfig(const char* fname)
{
    bool bRet = true;
    using namespace tinyxml2;
    /*XML parsing*/
    tinyxml2::XMLDocument xml_doc;
    XMLNode *xml_node;

    if (!checkExtension(fname, ".xml"))
    {
        LOG("<FAILED> Wrong file ext.\n");
        return false;
    }

    auto ret = xml_doc.LoadFile(fname);
    if (ret != XML_SUCCESS)
    {
        LOG("<FAILED> Loading file (%d)\n", ret);
        return false;
    }

    xml_node = xml_doc.FirstChild();

    int nWave = 1;
    char szNodeName[32] = { 0, };
    sprintf(szNodeName, "SLM_WaveNum");
    auto next = xml_node->FirstChildElement(szNodeName); // OffsetInDepth
    if (!next || XML_SUCCESS != next->QueryIntText(&nWave))
    {
        LOG("<FAILED> Not found node : \'%s\' (Integer) \n", szNodeName);
        bRet = false;
    }

    context_.waveNum = nWave;
    if (context_.wave_length) delete[] context_.wave_length;
    context_.wave_length = new Real[nWave];

    for (int i = 1; i <= nWave; i++) {
        sprintf(szNodeName, "SLM_WaveLength_%d", i);
        next = xml_node->FirstChildElement(szNodeName);
        if (!next || XML_SUCCESS != next->QueryDoubleText(&context_.wave_length[i - 1]))
        {
            LOG("<FAILED> Not found node : \'%s\' (Double) \n", szNodeName);
            bRet = false;
        }
    }

    sprintf(szNodeName, "SLM_PixelNumX");
    next = xml_node->FirstChildElement(szNodeName);
    if (!next || XML_SUCCESS != next->QueryIntText(&context_.pixel_number[_X]))
    {
        LOG("<FAILED> Not found node : \'%s\' (Integer) \n", szNodeName);
        bRet = false;
    }

    sprintf(szNodeName, "SLM_PixelNumY");
    next = xml_node->FirstChildElement(szNodeName);
    if (!next || XML_SUCCESS != next->QueryIntText(&context_.pixel_number[_Y]))
    {
        LOG("<FAILED> Not found node : \'%s\' (Integer) \n", szNodeName);
        bRet = false;
    }

    sprintf(szNodeName, "SLM_PixelPitchX");
    next = xml_node->FirstChildElement("SLM_PixelPitchX");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&context_.pixel_pitch[_X]))
    {
        LOG("<FAILED> Not found node : \'%s\' (Double) \n", szNodeName);
        bRet = false;
    }

    sprintf(szNodeName, "SLM_PixelPitchY");
    next = xml_node->FirstChildElement("SLM_PixelPitchY");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&context_.pixel_pitch[_Y]))
    {
        LOG("<FAILED> Not found node : \'%s\' (Double) \n", szNodeName);
        bRet = false;
    }

    // option
    next = xml_node->FirstChildElement("IMG_Rotation");
    if (!next || XML_SUCCESS != next->QueryBoolText(&imgCfg.rotate))
        imgCfg.rotate = false;
    next = xml_node->FirstChildElement("IMG_Merge");
    if (!next || XML_SUCCESS != next->QueryBoolText(&imgCfg.merge))
        imgCfg.merge = false;
    next = xml_node->FirstChildElement("IMG_Flip");
    if (!next || XML_SUCCESS != next->QueryIntText(&imgCfg.flip))
        imgCfg.flip = 0;
    next = xml_node->FirstChildElement("EyeLength");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.EyeLength))
        bRet = false;
    next = xml_node->FirstChildElement("EyePupilDiameter");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.EyePupilDiaMeter))
        bRet = false;
    next = xml_node->FirstChildElement("EyeBoxSizeScaleFactor");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.EyeBoxSizeScale))
        bRet = false;
    next = xml_node->FirstChildElement("EyeBoxSizeX");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.EyeBoxSize[_X]))
        bRet = false;
    next = xml_node->FirstChildElement("EyeBoxSizeY");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.EyeBoxSize[_Y]))
        bRet = false;
    next = xml_node->FirstChildElement("EyeBoxUnit");
    if (!next || XML_SUCCESS != next->QueryIntText(&rec_config.EyeBoxUnit))
        bRet = false;
    next = xml_node->FirstChildElement("EyeCenterX");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.EyeCenter[_X]))
        bRet = false;
    next = xml_node->FirstChildElement("EyeCenterY");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.EyeCenter[_Y]))
        bRet = false;
    next = xml_node->FirstChildElement("EyeCenterZ");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.EyeCenter[_Z]))
        bRet = false;
    next = xml_node->FirstChildElement("EyeFocusDistance");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.EyeFocusDistance))
        bRet = false;
    next = xml_node->FirstChildElement("ResultSizeScale");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.ResultSizeScale))
        bRet = false;
    next = xml_node->FirstChildElement("SimulationTo");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.SimulationTo))
        bRet = false;
    next = xml_node->FirstChildElement("SimulationFrom");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.SimulationFrom))
        bRet = false;
    next = xml_node->FirstChildElement("SimulationStep");
    if (!next || XML_SUCCESS != next->QueryIntText(&rec_config.SimulationStep))
        bRet = false;
    next = xml_node->FirstChildElement("SimulationMode");
    if (!next || XML_SUCCESS != next->QueryIntText(&rec_config.SimulationMode))
        bRet = false;
    next = xml_node->FirstChildElement("RatioAtRetina");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.RatioAtRetina))
        bRet = false;
    next = xml_node->FirstChildElement("RatioAtPupil");
    if (!next || XML_SUCCESS != next->QueryDoubleText(&rec_config.RatioAtPupil))
        bRet = false;
    next = xml_node->FirstChildElement("CreatePupilFieldImg");
    if (!next || XML_SUCCESS != next->QueryBoolText(&rec_config.CreatePupilFieldImg))
        bRet = false;
    next = xml_node->FirstChildElement("CenteringRetinalImg");
    if (!next || XML_SUCCESS != next->QueryBoolText(&rec_config.CenteringRetinaImg))
        bRet = false;

    context_.ss[_X] = context_.pixel_number[_X] * context_.pixel_pitch[_X];
    context_.ss[_Y] = context_.pixel_number[_Y] * context_.pixel_pitch[_Y];

    rec_config.EyeBoxSize = rec_config.EyeBoxSizeScale * rec_config.EyePupilDiaMeter * rec_config.EyeBoxSize;
    Initialize();

    LOG("**************************************************\n");
    LOG("                Read Config (Common)              \n");
    LOG("1) SLM Number of Waves : %d\n", context_.waveNum);
    for (uint i = 0; i < context_.waveNum; i++)
        LOG(" 1-%d) SLM Wave length : %e\n", i + 1, context_.wave_length[i]);
    LOG("2) SLM Resolution : %d x %d\n", context_.pixel_number[_X], context_.pixel_number[_Y]);
    LOG("3) SLM Pixel Pitch : %e x %e\n", context_.pixel_pitch[_X], context_.pixel_pitch[_Y]);
    LOG("4) Image Rotate : %s\n", imgCfg.rotate ? "Y" : "N");
    LOG("5) Image Flip : %s\n", (imgCfg.flip == FLIP::NONE) ? "NONE" :
        (imgCfg.flip == FLIP::VERTICAL) ? "VERTICAL" :
        (imgCfg.flip == FLIP::HORIZONTAL) ? "HORIZONTAL" : "BOTH");
    LOG("6) Image Merge : %s\n", imgCfg.merge ? "Y" : "N");
    LOG("**************************************************\n");

    return bRet;
}

bool ophRec::readImage(const char* path)
{
    const int pnX = context_.pixel_number[_X];
    const int pnY = context_.pixel_number[_Y];
    const int N = pnX * pnY;

    int w, h, bytesperpixel;
    bool ret = getImgSize(w, h, bytesperpixel, path);
    uchar* imgload = new uchar[w * h * bytesperpixel];

    int nLine = ((w * bytesperpixel) + 3) & ~3;
    int nSize = nLine * h;

    ret = loadAsImgUpSideDown(path, imgload);
    if (!ret) {
        LOG("Failed::Image Load: %s\n", path);
        return false;
    }
    LOG("Succeed::Image Load: %s\n", path);

    uchar *tmp = new uchar[nSize];
    memset(tmp, 0, sizeof(char) * nSize);

    if (w != pnX || h != pnY)
    {
        for (int ch = 0; ch < bytesperpixel; ch++)
            imgScaleBilinear(imgload, tmp, w, h, pnX, pnY, ch);
    }
    else
        memcpy(tmp, imgload, sizeof(char) * nSize);

    delete[] imgload;

    for (int ch = 0; ch < bytesperpixel; ch++)
    {
        int idx = bytesperpixel - 1 - ch;
        for (int i = 0; i < N; i++)
        {
            int src = i * bytesperpixel;
            complex_H[ch][i][_RE] = Real(tmp[src + idx]);
            complex_H[ch][i][_IM] = 0.0;
        }
    }
    delete[] tmp;
    return true;
}

bool ophRec::readImagePNA(const char *phase, const char *amplitude)
{
    const int pnX = context_.pixel_number[_X];
    const int pnY = context_.pixel_number[_Y];
    const int N = pnX * pnY;

    int w, h, bytesperpixel;
    bool ret = getImgSize(w, h, bytesperpixel, phase);
    uchar* imgload = new uchar[w * h * bytesperpixel];

    int nLine = ((w * bytesperpixel) + 3) & ~3;
    int nSize = nLine * h;

    ret = loadAsImgUpSideDown(phase, imgload);
    if (!ret) {
        LOG("Failed::Image Load: %s\n", phase);
        return false;
    }
    LOG("Succeed::Image Load: %s\n", phase);

    uchar *phaseTmp = new uchar[nSize];
    memset(phaseTmp, 0, sizeof(char) * nSize);

    if (w != pnX || h != pnY)
    {
        for (int ch = 0; ch < bytesperpixel; ch++)
            imgScaleBilinear(imgload, phaseTmp, w, h, pnX, pnY, ch);
    }
    else
        memcpy(phaseTmp, imgload, sizeof(char) * nSize);

    delete[] imgload;


    ret = getImgSize(w, h, bytesperpixel, amplitude);
    imgload = new uchar[w * h * bytesperpixel];

    nLine = ((w * bytesperpixel) + 3) & ~3;
    nSize = nLine * h;

    ret = loadAsImgUpSideDown(amplitude, imgload);
    if (!ret) {
        LOG("Failed::Image Load: %s\n", amplitude);
        return false;
    }
    LOG("Succeed::Image Load: %s\n", amplitude);

    uchar *ampTmp = new uchar[nSize];
    memset(ampTmp, 0, sizeof(char) * nSize);

    if (w != pnX || h != pnY)
    {
        for (int ch = 0; ch < bytesperpixel; ch++)
            imgScaleBilinear(imgload, ampTmp, w, h, pnX, pnY, ch);
    }
    else
        memcpy(ampTmp, imgload, sizeof(char) * nSize);

    delete[] imgload;

    Real PI2 = M_PI * 2;

    for (int ch = 0; ch < bytesperpixel; ch++)
    {
        int idx = bytesperpixel - 1 - ch;
        for (int i = 0; i < N; i++)
        {
            int src = i * bytesperpixel;
            Real p = Real(phaseTmp[src + idx]);
            Real a = Real(ampTmp[src + idx]);
            p = p / 255.0 * PI2 - M_PI; // -pi ~ pi
            a = a / 255.0; // 0 ~ 1
            Complex<Real> tmp(0, p);
            tmp.exp();
            complex_H[ch][i] = a * tmp;

        }
    }

    delete[] phaseTmp;
    delete[] ampTmp;
    return true;
}

bool ophRec::readImageRNI(const char *real, const char *imag)
{
    const int pnX = context_.pixel_number[_X];
    const int pnY = context_.pixel_number[_Y];
    const int N = pnX * pnY;

    int w, h, bytesperpixel;
    bool ret = getImgSize(w, h, bytesperpixel, real);
    uchar* imgload = new uchar[w * h * bytesperpixel];

    int nLine = ((w * bytesperpixel) + 3) & ~3;
    int nSize = nLine * h;

    ret = loadAsImgUpSideDown(real, imgload);
    if (!ret) {
        LOG("Failed::Image Load: %s\n", real);
        return false;
    }
    LOG("Succeed::Image Load: %s\n", real);

    uchar *realTmp = new uchar[nSize];
    memset(realTmp, 0, sizeof(char) * nSize);

    if (w != pnX || h != pnY)
    {
        for (int ch = 0; ch < bytesperpixel; ch++)
            imgScaleBilinear(imgload, realTmp, w, h, pnX, pnY, ch);
    }
    else
        memcpy(realTmp, imgload, sizeof(char) * nSize);

    delete[] imgload;


    ret = getImgSize(w, h, bytesperpixel, imag);
    imgload = new uchar[w * h * bytesperpixel];
    nLine = ((w * bytesperpixel) + 3) & ~3;
    nSize = nLine * h;

    ret = loadAsImgUpSideDown(imag, imgload);
    if (!ret) {
        LOG("Failed::Image Load: %s\n", imag);
        return false;
    }
    LOG("Succeed::Image Load: %s\n", imag);

    uchar *imagTmp = new uchar[nSize];
    memset(imagTmp, 0, sizeof(char) * nSize);

    if (w != pnX || h != pnY)
    {
        for (int ch = 0; ch < bytesperpixel; ch++)
            imgScaleBilinear(imgload, imagTmp, w, h, pnX, pnY, ch);
    }
    else
        memcpy(imagTmp, imgload, sizeof(char) * nSize);

    delete[] imgload;

    for (int ch = 0; ch < bytesperpixel; ch++)
    {
        int idx = bytesperpixel - 1 - ch;
        for (int i = 0; i < N; i++)
        {
            int src = i * bytesperpixel;
            complex_H[ch][i][_RE] = (Real)realTmp[src + idx] / 255.0;
            complex_H[ch][i][_IM] = (Real)imagTmp[src + idx] / 255.0;
        }
    }
    delete[] realTmp;
    delete[] imagTmp;
    return true;
}

void ophRec::GetPupilFieldFromHologram()
{
    LOG("Propagation to observer plane\n");

    const int channel = context_.waveNum;
    const int pnX = context_.pixel_number[_X];
    const int pnY = context_.pixel_number[_Y];
    field_set_.resize(channel);
    pp_set_.resize(channel);
    fftw_complex *in = nullptr;
    fftw_complex *out = nullptr;
    fftw_plan fftw_plan_fwd = fftw_plan_dft_2d(pnY, pnX, in, out, FFTW_FORWARD, FFTW_ESTIMATE);

    for (int ch = 0; ch < channel; ch++)
    {
        Propagation_Fresnel_FFT(ch);
    }

    fftw_destroy_plan(fftw_plan_fwd);
}

void ophRec::GetPupilFieldFromVWHologram()
{
    LOG("Propagation to observer plane\n");

    const int nChannel = context_.waveNum;
    const int pnX = context_.pixel_number[_X];
    const int pnY = context_.pixel_number[_Y];
    const int N = pnX * pnY;
    const Real ppX = context_.pixel_pitch[_X];
    const Real ppY = context_.pixel_pitch[_Y];

    field_set_.resize(nChannel);
    pn_set_.resize(nChannel);
    pp_set_.resize(nChannel);

    fftw_complex *in = nullptr, *out = nullptr;
    fftw_plan fft_plan_fwd = fftw_plan_dft_2d(pnY, pnX, in, out, FFTW_FORWARD, FFTW_ESTIMATE);

    double prop_z = rec_config.EyeCenter[_Z];
    double f_field = rec_config.EyeCenter[_Z];


    Real ssX = pnX * ppX;
    Real ssY = pnY * ppY;


    for (int ctr = 0; ctr < nChannel; ctr++)
    {
        LOG("Color Number: %d\n", ctr + 1);

        Complex<Real>* u = complex_H[ctr];
        field_set_[ctr] = new Complex<Real>[N];
        memset(field_set_[ctr], 0.0, sizeof(Complex<Real>) * N);

        Real lambda = context_.wave_length[ctr];

        Real k = 2 * M_PI / lambda;
        Real kk = k / (prop_z * 2);
        Real kpropz = k * prop_z;
        Real lambdapropz = lambda * prop_z;
        Real ss_res_x = fabs(lambdapropz / ppX);
        Real ss_res_y = fabs(lambdapropz / ppY);
        Real hss_res_x = ss_res_x / 2.0;
        Real hss_res_y = ss_res_y / 2.0;
        Real pp_res_x = ss_res_x / Real(pnX);
        Real pp_res_y = ss_res_y / Real(pnY);
        Real absppX = fabs(lambdapropz / (4 * ppX));
        Real absppY = fabs(lambdapropz / (4 * ppY));

        int loopi;
#pragma omp parallel for private(loopi) 
        for (loopi = 0; loopi < N; loopi++)
        {
            int x = loopi % pnX;
            int y = loopi / pnX;

            double xx_src = (-ssX / 2.0) + (ppX * double(x));
            double yy_src = (ssY / 2.0) - ppY - (ppY * double(y));

            if (f_field != prop_z)
            {
                double effective_f = f_field * prop_z / (f_field - prop_z);
                double sval = (xx_src*xx_src) + (yy_src*yy_src);
                sval *= M_PI / lambda / effective_f;
                Complex<Real> kernel(0, sval);
                kernel.exp();
                //exponent_complex(&kernel);

                double anti_aliasing_mask = fabs(xx_src) < fabs(lambda*effective_f / (4 * ppX)) ? 1 : 0;
                anti_aliasing_mask *= fabs(yy_src) < fabs(lambda*effective_f / (4 * ppY)) ? 1 : 0;

                field_set_[ctr][x + y * pnX] = u[x + y * pnX] * kernel * anti_aliasing_mask;


            }
            else {

                field_set_[ctr][x + y * pnX] = u[x + y * pnX];

            }
        }
        //delete[] fringe_[ctr];
        //free(fringe_[ctr]);

        fft2(field_set_[ctr], field_set_[ctr], pnX, pnY, FFTW_FORWARD, false);



#pragma omp parallel for private(loopi) 
        for (loopi = 0; loopi < N; loopi++)
        {
            int x = loopi % pnX;
            int y = loopi / pnX;

            double xx_res = (-ss_res_x / 2.0) + (pp_res_x * double(x));
            double yy_res = (ss_res_y / 2.0) - pp_res_y - (pp_res_y * double(y));

            Complex<Real> tmp1(0, k*prop_z);
            tmp1.exp();
            //exponent_complex(&tmp1);

            Complex<Real> tmp2(0, lambda*prop_z);

            double ssval = (xx_res*xx_res) + (yy_res*yy_res);
            ssval *= k / (2 * prop_z);
            Complex<Real> tmp3(0, ssval);
            //exponent_complex(&tmp3);
            tmp3.exp();

            Complex<Real> coeff = tmp1 / tmp2 * tmp3;

            field_set_[ctr][x + y * pnX] *= coeff;

        }
        pp_set_[ctr][0] = pp_res_x;
        pp_set_[ctr][1] = pp_res_y;

    }

    fftw_destroy_plan(fft_plan_fwd);
}

void ophRec::ASM_Propagation()
{
    const int pnX = context_.pixel_number[_X];
    const int pnY = context_.pixel_number[_Y];
    const int N = pnX * pnY;
    const int nWave = context_.waveNum;

    const Real ppX = context_.pixel_pitch[_X];
    const Real ppY = context_.pixel_pitch[_Y];

    const Real simFrom = rec_config.SimulationFrom;
    const Real simTo = rec_config.SimulationTo;
    const int simStep = rec_config.SimulationStep;
    const Real simGap = (simStep > 1) ? (simTo - simFrom) / (simStep - 1) : 0;

    const Real tx = 1 / ppX;
    const Real ty = 1 / ppY;
    const Real dx = tx / pnX;
    const Real dy = ty / pnY;

    const Real htx = tx / 2;
    const Real hty = ty / 2;
    const Real hdx = dx / 2;
    const Real hdy = dy / 2;
    const Real baseX = -htx + hdx;
    const Real baseY = -hty + hdy;

    Complex<Real>* tmp = new Complex<Real>[N];
    Complex<Real>* src = nullptr;
    Complex<Real>* dst = new Complex<Real>[N];
    Complex<Real>** kernels = new Complex<Real>*[nWave];// [N];
    for (int i = 0; i < nWave; i++)
    {
        kernels[i] = new Complex<Real>[N];
    }

    LOG("%s : Get Spatial Kernel\n", __FUNCTION__);
    auto begin = CUR_TIME;
    for (int ch = 0; ch < nWave; ch++)
    {
        const Real lambda = context_.wave_length[ch];
        const Real k = 2 * M_PI / lambda;
        src = complex_H[ch];
        
        // Get Spatial Kernel
        int i;
#ifdef _OPENMP
#pragma omp parallel for private(i) firstprivate(pnX, lambda, dx, dy, baseX, baseY)
#endif
        for (i = 0; i < N; i++)
        {
            int x = i % pnX;
            int y = i / pnX;

            Real curX = baseX + (x * dx);
            Real curY = baseY + (y * dy);
            Real xx = curX * lambda;
            Real yy = curY * lambda;
            Real powxx = xx * xx;
            Real powyy = yy * yy;

            kernels[ch][i][_RE] = 0;
            kernels[ch][i][_IM] = sqrt(1 - powxx - powyy);
        }
    }
    LOG(" => %lf(s)\n", ELAPSED_TIME(begin, CUR_TIME));
    LOG("%s : Simultation\n", __FUNCTION__);
    begin = CUR_TIME;   

    for (int step = 0; step < simStep; step++)
    {
        Real min = MAX_DOUBLE, max = MIN_DOUBLE;
        for (int ch = 0; ch < nWave; ch++)
        {
            const Real lambda = context_.wave_length[ch];
            const Real k = 2 * M_PI / lambda;
            src = complex_H[ch];
            fft2(src, tmp, pnX, pnY, FFTW_FORWARD, false);
            Real z = simFrom + (step * simGap);
            Real kz = k * z;

            Real* encode = new Real[N];
            uchar* normal = new uchar[N];

            //m_vecEncoded[step] = new Real[N];
            //m_vecNormalized[step] = new uchar[N];

            for (int i = 0; i < N; i++)
            {
                Complex<Real> kernel = kernels[ch][i];
                kernel[_IM] *= kz;
                kernel.exp();
                tmp[i] *= kernel;
            }

            fft2(tmp, dst, pnX, pnY, FFTW_BACKWARD, true);

            for (int i = 0; i < N; i++)
            {
                encode[i] = dst[i].mag();

                if (min > encode[i])
                    min = encode[i];
                if (max < encode[i])
                    max = encode[i];
            }

            m_vecEncoded.push_back(encode);
            m_vecNormalized.push_back(normal);
        }

        LOG("step: %d => max: %e / min: %e\n", step, max, min);
        if (nWave == 3)
        {
            for (int ch = 0; ch < nWave; ch++)
            {
                int idx = step * nWave + ch;
                normalize(m_vecEncoded[idx], m_vecNormalized[idx], pnX, pnY, max, min);
            }
        }
        else
            normalize(m_vecEncoded[step], m_vecNormalized[step], pnX, pnY);
    }

    m_oldSimStep = simStep;
    fftFree();
    LOG(" => %lf(s)\n", ELAPSED_TIME(begin, CUR_TIME));

    for (int i = 0; i < nWave; i++)
        delete[] kernels[i];
    delete[] kernels;
    delete[] tmp;
    delete[] dst;


}

void ophRec::Propagation_Fresnel_FFT(int chnum)
{
    LOG("Color Number: %d\n", chnum + 1);

    const int pnX = context_.pixel_number[_X];
    const int pnY = context_.pixel_number[_Y];
    const int N = pnX * pnY;
    Real ppX = context_.pixel_pitch[_X];
    Real ppY = context_.pixel_pitch[_Y];
    Real ppX4 = ppX * 4;
    Real ppY4 = ppY * 4;
    Real lambda = context_.wave_length[chnum];
    Real ssX = pnX * ppX;
    Real ssY = pnY * ppY;
    Real hssX = ssX / 2.0;
    Real hssY = ssY / 2.0;
    Real prop_z = rec_config.EyeCenter[_Z];
    vec2 cxy = vec2(0);

    Real k = 2 * M_PI / lambda;
    Real kk = k / (prop_z * 2);
    Real kpropz = k * prop_z;
    Real lambdapropz = lambda * prop_z;
    Real ss_res_x = fabs(lambdapropz / ppX);
    Real ss_res_y = fabs(lambdapropz / ppY);
    Real hss_res_x = ss_res_x / 2.0;
    Real hss_res_y = ss_res_y / 2.0;
    Real pp_res_x = ss_res_x / Real(pnX);
    Real pp_res_y = ss_res_y / Real(pnY);

    Complex<Real>* tmp = complex_H[chnum];
    field_set_[chnum] = new Complex<Real>[N];
    memset(field_set_[chnum], 0.0, sizeof(Complex<Real>) * N);

    //Real xx_src, yy_src, xx_res, yy_res;
    //int x, y;

    Real absppX = fabs(lambdapropz / (ppX4));
    Real absppY = fabs(lambdapropz / (ppY4));

    int i;
#pragma omp parallel for private(i) 
    for (i = 0; i < N; i++)
    {
        int x = i % pnX;
        int y = i / pnX;

        Real xx_src = -hssX + (ppX * Real(x));
        Real yy_src = hssY - ppY - (ppY * Real(y));
        Real xxx = xx_src - cxy[_X];
        Real yyy = yy_src - cxy[_Y];

        Real sval = xxx * xxx + yyy * yyy;
        sval *= kk;
        Complex<Real> kernel(0, sval);
        kernel.exp();
        //exponent_complex(&kernel);

        Real anti_aliasing_mask = fabs(xxx) < absppX ? 1 : 0;
        anti_aliasing_mask *= fabs(yyy) < absppY ? 1 : 0;

        field_set_[chnum][x + y * pnX] = tmp[x + y * pnX] * kernel * anti_aliasing_mask;

    }
    //free(fringe_[chnum]);

    //fftw_complex *in = nullptr, *out = nullptr;
    fft2(field_set_[chnum], field_set_[chnum], pnX, pnY, FFTW_FORWARD, false);

#pragma omp parallel for private(i) 
    for (i = 0; i < N; i++)
    {
        int x = i % pnX;
        int y = i / pnX;

        Real xx_res = -hss_res_x + (pp_res_x * Real(x));
        Real yy_res = hss_res_y - pp_res_y - (pp_res_y * Real(y));
        Real xxx = xx_res - cxy[_X];
        Real yyy = yy_res - cxy[_Y];

        Complex<Real> tmp1(0, kpropz);
        tmp1.exp();
        //exponent_complex(&tmp1);

        Complex<Real> tmp2(0, lambdapropz);

        Real ssval = xxx * xxx + yyy * yyy;
        ssval *= kk;
        Complex<Real> tmp3(0, ssval);
        tmp3.exp();
        //exponent_complex(&tmp3);

        Complex<Real> coeff = tmp1 / tmp2 * tmp3;

        field_set_[chnum][x + y * pnX] *= coeff;

    }

    //pn_set_[chnum] = PIXEL_NUMBER;
    pp_set_[chnum][_X] = pp_res_x;
    pp_set_[chnum][_Y] = pp_res_y;
}

void ophRec::Perform_Simulation()
{
    LOG("Simulation start\n");
    FILE *fp;
    const int pnX = context_.pixel_number[_X];
    const int pnY = context_.pixel_number[_Y];
    const Real ppX = context_.pixel_pitch[_X];
    const Real ppY = context_.pixel_pitch[_Y];
    const int nChannel = context_.waveNum;
    const int simStep = rec_config.SimulationStep;
    const Real simFrom = rec_config.SimulationFrom;
    const Real simTo = rec_config.SimulationTo;
    const int simMode = rec_config.SimulationMode;
    vec2 boxSize = rec_config.EyeBoxSize;
    vec3 eyeCenter = rec_config.EyeCenter;
    Real eyeLen = rec_config.EyeLength;
    Real eyeFocusDistance = rec_config.EyeFocusDistance;
    bool bCreatePupilImg = rec_config.CreatePupilFieldImg;
    bool bCenteringRetinaImg = rec_config.CenteringRetinaImg;
    Real resultSizeScale = rec_config.ResultSizeScale;
    Real eyePupil = rec_config.EyePupilDiaMeter;
    bool bSimPos[3];
    Real ratioAtRetina = rec_config.RatioAtRetina;

    memcpy(&bSimPos[0], rec_config.SimulationPos, sizeof(bSimPos));

    vec3 var_step;
    std::vector<vec3> var_vals;
    var_vals.resize(simStep);

    if (simStep > 1)
    {
        var_step = (simTo - simFrom) / (simStep - 1);
        for (int i = 0; i < simStep; i++)
            var_vals[i] = simFrom + var_step * i;

    }
    else
        var_vals[0] = (simTo + simFrom) / 2.0;

    Real lambda, k;
    int pn_e_x, pn_e_y;
    Real pp_e_x, pp_e_y, ss_e_x, ss_e_y;
    int pn_p_x, pn_p_y;
    Real pp_p_x, pp_p_y, ss_p_x, ss_p_y;
    vec2 eye_box_range_x, eye_box_range_y;
    ivec2 eye_box_range_idx, eye_box_range_idy;
    ivec2 eye_shift_by_pn;

    field_ret_set_.resize(nChannel);
    pn_ret_set_.resize(nChannel);
    pp_ret_set_.resize(nChannel);
    ss_ret_set_.resize(nChannel);
    recon_set.resize(simStep * nChannel);
    img_set.resize(simStep * nChannel);
    img_size.resize(simStep * nChannel);
    focus_recon_set.resize(simStep);
    focus_img_set.resize(simStep);
    focus_img_size.resize(simStep);

    std::string varname2;

    for (int vtr = 0; vtr < simStep; vtr++)
    {
        if (simMode == 0) {
            eyeFocusDistance = var_vals[vtr][_X];
        }
        else {
            if (bSimPos[_X]) eyeCenter[_X] = var_vals[vtr][_X];
            if (bSimPos[_Y]) eyeCenter[_Y] = var_vals[vtr][_X];
            if (bSimPos[_Z]) eyeCenter[_Z] = var_vals[vtr][_X];
        }

        for (int ctr = 0; ctr < nChannel; ctr++)
        {
            lambda = context_.wave_length[ctr];
            k = 2 * M_PI / lambda;

            pn_e_x = pnX;
            pn_e_y = pnY;
            pp_e_x = pp_set_[ctr][_X];
            pp_e_y = pp_set_[ctr][_Y];
            ss_e_x = Real(pn_e_x) * pp_e_x;
            ss_e_y = Real(pn_e_y) * pp_e_y;

            eye_shift_by_pn[0] = round(eyeCenter[_X] / pp_e_x);
            eye_shift_by_pn[1] = round(eyeCenter[_Y] / pp_e_y);

            Complex<Real>* hh_e_shift = new Complex<Real>[pn_e_x * pn_e_y];
            memset(hh_e_shift, 0.0, sizeof(Complex<Real>) * pn_e_x * pn_e_y);
            circshift(field_set_[ctr], hh_e_shift, -eye_shift_by_pn[0], eye_shift_by_pn[1], pn_e_x, pn_e_y);


            if (rec_config.EyeBoxUnit == 0)
            {
                eye_box_range_x[0] = -boxSize[_X] / 2.0;
                eye_box_range_x[1] = boxSize[_X] / 2.0;
                eye_box_range_y[0] = -boxSize[_Y] / 2.0;
                eye_box_range_y[1] = boxSize[_Y] / 2.0;
                eye_box_range_idx[0] = floor((eye_box_range_x[0] + ss_e_x / 2.0) / pp_e_x);
                eye_box_range_idx[1] = floor((eye_box_range_x[1] + ss_e_x / 2.0) / pp_e_x);
                eye_box_range_idy[0] = pn_e_y - floor((eye_box_range_y[1] + ss_e_y / 2.0) / pp_e_y);
                eye_box_range_idy[1] = pn_e_y - floor((eye_box_range_y[0] + ss_e_y / 2.0) / pp_e_y);

            }
            else {

                int temp = floor((pn_e_x - boxSize[_X]) / 2.0);
                eye_box_range_idx[0] = temp;
                eye_box_range_idx[1] = temp + boxSize[_X] - 1;
                temp = floor((pn_e_y - boxSize[_Y]) / 2.0);
                eye_box_range_idy[0] = temp;
                eye_box_range_idy[1] = temp + boxSize[_Y] - 1;
            }

            pn_p_x = eye_box_range_idx[1] - eye_box_range_idx[0] + 1;
            pn_p_y = eye_box_range_idy[1] - eye_box_range_idy[0] + 1;
            pp_p_x = pp_e_x;
            pp_p_y = pp_e_y;
            ss_p_x = pn_p_x * pp_p_x;
            ss_p_y = pn_p_y * pp_p_y;

            int N = pn_p_x * pn_p_y;
            int N2 = pn_e_x * pn_e_y;
            Complex<Real>* hh_p = new Complex<Real>[N];
            memset(hh_p, 0.0, sizeof(Complex<Real>) * N);

            int cropidx = 0;

            for (int p = 0; p < N2; p++)
            {
                int x = p % pn_e_x;
                int y = p / pn_e_x;

                if (x >= eye_box_range_idx[0] - 1 && x <= eye_box_range_idx[1] - 1 && y >= eye_box_range_idy[0] - 1 && y <= eye_box_range_idy[1] - 1)
                {
                    int xx = cropidx % pn_p_x;
                    int yy = cropidx / pn_p_x;
                    hh_p[yy*pn_p_x + xx] = hh_e_shift[p];
                    cropidx++;
                }
            }
            delete[] hh_e_shift;

            Real f_eye = eyeLen * (eyeCenter[_Z] - eyeFocusDistance) / (eyeLen + (eyeCenter[_Z] - eyeFocusDistance));
            Real effective_f = f_eye * eyeLen / (f_eye - eyeLen);

            Complex<Real>* hh_e_ = new Complex<Real>[N];
            memset(hh_e_, 0.0, sizeof(Complex<Real>) * N);

            int loopp;
            //#pragma omp parallel for private(loopp)   
            for (loopp = 0; loopp < N; loopp++)
            {
                int x = loopp % pn_p_x;
                int y = loopp / pn_p_x;

                Real XE = -ss_p_x / 2.0 + (pp_p_x *x);
                Real YE = ss_p_y / 2.0 - pp_p_y - (pp_p_y * y);

                Real sval = (XE*XE) + (YE*YE);
                sval *= M_PI / lambda / effective_f;
                Complex<Real> eye_propagation_kernel(0, sval);
                eye_propagation_kernel.exp();

                Real eye_lens_anti_aliasing_mask = fabs(XE) < fabs(lambda*effective_f / (4 * pp_e_x)) ? 1.0 : 0.0;
                eye_lens_anti_aliasing_mask *= fabs(YE) < fabs(lambda*effective_f / (4 * pp_e_y)) ? 1.0 : 0.0;

                Real eye_pupil_mask = sqrt(XE*XE + YE * YE) < (eyePupil / 2.0) ? 1.0 : 0.0;

                hh_e_[x + y * pn_p_x] = hh_p[x + y * pn_p_x] * eye_propagation_kernel * eye_lens_anti_aliasing_mask * eye_pupil_mask;
            }

            delete[] hh_p;

            fft2(hh_e_, hh_e_, pn_p_x, pn_p_y, FFTW_FORWARD, false);

            Real pp_ret_x, pp_ret_y;
            int pn_ret_x, pn_ret_y;
            vec2 ret_size_xy;

            pp_ret_x = lambda * eyeLen / ss_p_x;
            pp_ret_y = lambda * eyeLen / ss_p_y;
            pn_ret_x = pn_p_x;
            pn_ret_y = pn_p_y;
            ret_size_xy[0] = pp_ret_x * pn_ret_x;
            ret_size_xy[1] = pp_ret_y * pn_ret_y;

            field_ret_set_[ctr] = new Real[pn_p_x * pn_p_y];
            memset(field_ret_set_[ctr], 0.0, sizeof(Real)*pn_p_x*pn_p_y);

            //#pragma omp parallel for private(loopp)   
            for (loopp = 0; loopp < pn_p_x*pn_p_y; loopp++)
            {
                int x = loopp % pn_p_x;
                int y = loopp / pn_p_x;

                Real XR = ret_size_xy[0] / 2.0 + (pp_ret_x * x);
                Real YR = ret_size_xy[1] / 2.0 - pp_ret_y - (pp_ret_y * y);

                Real sval = (XR*XR) + (YR*YR);
                sval *= k / (2 * eyeLen);
                Complex<Real> val1(0, sval);
                val1.exp();

                Complex<Real> val2(0, k * eyeLen);
                val2.exp();
                Complex<Real> val3(0, lambda * eyeLen);

                field_ret_set_[ctr][x + pn_p_x * y] = (hh_e_[x + pn_p_x * y] * (val1 * val2 / val3)).mag();

            }
            delete[] hh_e_;

            pp_ret_set_[ctr] = vec2(pp_ret_x, pp_ret_y);
            pn_ret_set_[ctr] = ivec2(pn_ret_x, pn_ret_y);
            ss_ret_set_[ctr] = pp_ret_set_[ctr] * pn_ret_set_[ctr];

            if (bCreatePupilImg)
            {
                Real pp_min = (pp_e_x > pp_e_y) ? pp_e_y : pp_e_x;
                Real ss_max = (ss_e_x > ss_e_y) ? ss_e_x : ss_e_y;
                Real pn_tar = ceil(ss_max / pp_min);
                pp_min = ss_max / pn_tar;
                Real pn_e_tar_x = round(ss_e_x / pp_min);
                Real pn_e_tar_y = round(ss_e_y / pp_min);

                Real resize_scale_x = pn_e_tar_x * resultSizeScale;
                Real resize_scale_y = pn_e_tar_y * resultSizeScale;

                int N = resize_scale_x * resize_scale_y;

                recon_set[vtr * nChannel + ctr] = new Real[N];
                img_set[vtr * nChannel + ctr] = new uchar[N];

                memset(recon_set[vtr * nChannel + ctr], 0.0, sizeof(Real) * N);
                memset(img_set[vtr * nChannel + ctr], 0, sizeof(uchar) * N);

                GetPupilFieldImage(field_set_[ctr], recon_set[vtr * nChannel + ctr]
                    , pn_e_x, pn_e_y, pp_e_x, pp_e_y, resize_scale_x, resize_scale_y);

                std::string fname = std::string("./").append("").append("/FIELD/");
                fname = fname.append("FIELD_COLOR_").append(std::to_string(ctr + 1)).append("_").append("").append("_SAT_").append("").append("_").append(std::to_string(vtr + 1)).append(".bmp");
                normalize(recon_set[vtr * nChannel + ctr], img_set[vtr * nChannel + ctr], (int)resize_scale_x, (int)resize_scale_y);
                img_size[vtr * nChannel + ctr][_X] = (int)resize_scale_x;
                img_size[vtr * nChannel + ctr][_Y] = (int)resize_scale_y;
            }

        }   // end of ctr

        Real pnx_max = 0.0, pny_max = 0.0;
        for (int i = 0; i < nChannel; i++)
        {
            pnx_max = (pn_ret_set_[i][0] > pnx_max ? pn_ret_set_[i][0] : pnx_max);
            pny_max = (pn_ret_set_[i][1] > pny_max ? pn_ret_set_[i][1] : pny_max);
        }

        Real retinal_image_shift_x = eyeCenter[_X] * eyeLen / eyeCenter[_Z];
        Real retinal_image_shift_y = eyeCenter[_Y] * eyeLen / eyeCenter[_Z];

        res_set_.resize(nChannel);
        res_set_norm_255_.resize(nChannel);

        int loopi;
        //#pragma omp parallel for private(loopi)   
        for (loopi = 0; loopi < nChannel; loopi++)
        {
            Real lambda = context_.wave_length[loopi];
            Real* hh_ret_ = new Real[pn_ret_set_[loopi][0] * pn_ret_set_[loopi][1]];
            memset(hh_ret_, 0.0, sizeof(Real)*pn_ret_set_[loopi][0] * pn_ret_set_[loopi][1]);

            if (bCenteringRetinaImg)
            {
                Real retinal_image_shift_by_pn_x = round(retinal_image_shift_x / pp_ret_set_[loopi][0]);
                Real retinal_image_shift_by_pn_y = round(retinal_image_shift_y / pp_ret_set_[loopi][1]);

                circshift(field_ret_set_[loopi], hh_ret_, -retinal_image_shift_by_pn_x, retinal_image_shift_by_pn_y, pn_ret_set_[loopi][0], pn_ret_set_[loopi][1]);

            }
            else
                hh_ret_ = field_ret_set_[loopi];

            delete[] field_ret_set_[loopi];

            int size = (int)(pnx_max * pny_max);
            res_set_[loopi] = new Real[size];
            memset(res_set_[loopi], 0.0, sizeof(Real) * size);
            ScaleBilnear(hh_ret_, res_set_[loopi], pn_ret_set_[loopi][0], pn_ret_set_[loopi][1], pnx_max, pny_max, lambda * lambda);

        }

        Real maxvalue = res_set_[0][0];
        Real minvalue = res_set_[0][0];
        for (int i = 0; i < nChannel; i++)
        {
            for (int j = 0; j < pnx_max*pny_max; j++)
            {
                maxvalue = res_set_[i][j] > maxvalue ? res_set_[i][j] : maxvalue;
                minvalue = res_set_[i][j] < minvalue ? res_set_[i][j] : minvalue;
            }
        }

        for (int j = 0; j < pnx_max*pny_max; j++)
        {
            res_set_[0][j] = (res_set_[0][j] - minvalue) / (maxvalue - minvalue) * 255;
        }

        //#pragma omp parallel for private(loopi)   
        for (loopi = 0; loopi < nChannel; loopi++)
        {
            for (int j = 0; j < pnx_max*pny_max; j++)
            {
                if (res_set_[loopi][j] > ratioAtRetina * maxvalue)
                    res_set_[loopi][j] = ratioAtRetina * maxvalue;

                res_set_[loopi][j] = (res_set_[loopi][j] - minvalue) / (ratioAtRetina*maxvalue - minvalue);

            }
        }

        Real ret_size_x = pnx_max * resultSizeScale;
        Real ret_size_y = pny_max * resultSizeScale;

        int size = (int)(ret_size_x * ret_size_y);

        //#pragma omp parallel for private(loopi)           
        for (loopi = 0; loopi < nChannel; loopi++)
        {
            Real* res_set_norm = new Real[size];
            memset(res_set_norm, 0.0, sizeof(Real) * size);

            ScaleBilnear(res_set_[loopi], res_set_norm, pnx_max, pny_max, ret_size_x, ret_size_y);

            res_set_norm_255_[loopi] = new Real[size];
            memset(res_set_norm_255_[loopi], 0.0, sizeof(Real) * size);

            rotateCCW180(res_set_norm, res_set_norm_255_[loopi], ret_size_x, ret_size_y, 255.0);

            delete[] res_set_norm;
        }

        for (int i = 0; i < nChannel; i++)
            delete[] res_set_[i];

        int N = ret_size_x * ret_size_y;

        focus_recon_set[vtr] = new Real[N * nChannel];
        focus_img_set[vtr] = new uchar[N * nChannel];
        memset(focus_recon_set[vtr], 0.0, sizeof(Real) * N * nChannel);
        memset(focus_img_set[vtr], 0, sizeof(uchar) * N * nChannel);

        if (nChannel == 1)
            memcpy(focus_recon_set[vtr], res_set_norm_255_[0], sizeof(Real)*ret_size_x*ret_size_y);
        else
            reArrangeChannel(res_set_norm_255_, focus_recon_set[vtr], ret_size_x, ret_size_y, nChannel);

        std::string fname = std::string("./").append("").append("/").append("").append("_SAT_").append("").append("_").append(varname2).append("_").append(std::to_string(vtr + 1)).append(".bmp");

        normalize(focus_recon_set[vtr], focus_img_set[vtr], ret_size_x, ret_size_y);

        focus_img_size[vtr][_X] = (int)ret_size_x;
        focus_img_size[vtr][_Y] = (int)ret_size_y;

        m_vecEncoded.push_back(focus_recon_set[vtr]);
        m_vecNormalized.push_back(focus_img_set[vtr]);


        for (int i = 0; i < nChannel; i++)
            delete[] res_set_norm_255_[i];
    } // end of vtr
}

bool ophRec::save(const char * fname, uint8_t bitsperpixel, uchar* src, uint px, uint py)
{
    bool bOK = false;

    if (fname == nullptr) return bOK;

    uchar* source = src;
    bool bAlloc = false;
    const uint nChannel = context_.waveNum;

    ivec2 p(px, py);
    if (px == 0 && py == 0)
        p = ivec2(context_.pixel_number[_X], context_.pixel_number[_Y]);


    std::string file = fname;
    std::replace(file.begin(), file.end(), '\\', '/');

    // split path
    std::vector<std::string> components;
    std::stringstream ss(file);
    std::string item;
    char token = '/';

    while (std::getline(ss, item, token)) {
        components.push_back(item);
    }

    std::string dir;

    for (size_t i = 0; i < components.size() - 1; i++)
    {
        dir += components[i];
        dir += "/";
    }

    std::string filename = components[components.size() - 1];

    // find extension
    bool hasExt;
    size_t ext_pos = file.rfind(".");
    hasExt = (ext_pos == string::npos) ? false : true;

    if (!hasExt)
        filename.append(".bmp");

    std::string fullpath = dir + filename;

    if (nChannel == 1) {
        saveAsImg(fullpath.c_str(), bitsperpixel, src, p[_X], p[_Y]);
    }
    else if (nChannel == 3) {
        if (imgCfg.merge) {
            uint nSize = (((p[_X] * bitsperpixel >> 3) + 3) & ~3) * p[_Y];
            uchar *source = new uchar[nSize];
            bAlloc = true;
            for (uint i = 0; i < nChannel; i++) {
                mergeColor(i, p[_X], p[_Y], src, source);
            }
            saveAsImg(fullpath.c_str(), bitsperpixel, source, p[_X], p[_Y]);
            if (bAlloc) delete[] source;
        }
        else {
            char path[FILENAME_MAX] = { 0, };
            sprintf(path, "%s%s", dir.c_str(), filename.c_str());
            saveAsImg(path, bitsperpixel / nChannel, src, p[_X], p[_Y]);
        }
    }
    else return false;

    return bOK;
}

void ophRec::SaveImage(const char *path, const char *ext)
{
    int nSimStep = rec_config.SimulationStep;
    int nChannel = context_.waveNum;
    bool bCreatePupilImg = rec_config.CreatePupilFieldImg;
    Real simTo = rec_config.SimulationTo;
    Real simFrom = rec_config.SimulationFrom;
    Real step = 0.0;

    int pnX;
    int pnY;

    if (m_idx == 0)
    {
        pnX = context_.pixel_number[_X];
        pnY = context_.pixel_number[_Y];
    }
    else
    {
        pnX = focus_img_size[0][_X];
        pnY = focus_img_size[0][_Y];
    }
    if (nSimStep > 1)
    {
        step = (simTo - simFrom) / (nSimStep - 1);
    }

    char tmpPath[FILENAME_MAX] = { 0, };
    bool bMultiStep = nSimStep > 1 ? true : false;
    uint nSize = (((pnX * nChannel) + 3) & ~3) * pnY;
    uchar *tmp = new uchar[nSize];

    for (int i = 0; i < nSimStep; i++)
    {
        sprintf(tmpPath, "%s\\FOCUS_%.4f.%s", path, bMultiStep ?
            simFrom + (step * i) : (simFrom + simTo) / 2, ext);

        if (nChannel == 3)
        {
            if (imgCfg.merge)
            {
                for (int ch = 0; ch < nChannel; ch++)
                {
                    mergeColor(ch, pnX, pnY, m_vecNormalized[i * nChannel + ch], tmp);
                }
                saveAsImg(tmpPath, 8 * nChannel, tmp, pnX, pnY); // save RGB
            }
            else
            {
                for (int ch = 0; ch < nChannel; ch++)
                {
                    memset(tmp, 0, sizeof(uchar) * nSize);
                    sprintf(tmpPath, "%s\\FOCUS_%.4f (%d).%s", path, bMultiStep ? simFrom + step * i : (simFrom + simTo) / 2, ch, ext);
                    mergeColor(ch, pnX, pnY, m_vecNormalized[i * nChannel + ch], tmp);
                    saveAsImg(tmpPath, 8 * nChannel, tmp, pnX, pnY); // save RGB
                }
            }
        }
        else
        {
            memcpy(tmp, m_vecNormalized[i], sizeof(uchar) * nSize);
            saveAsImg(tmpPath, 8 * nChannel, tmp, pnX, pnY); // save Grayscale
        }
    }
    delete[] tmp;
}

void ophRec::GetPupilFieldImage(Complex<Real>* src, Real* dst, int pnx, int pny, Real ppx, Real ppy, Real scaleX, Real scaleY)
{
    const int N = pnx * pny;
    Real ratioAtPupil = rec_config.RatioAtPupil;
    Real eyePupil = rec_config.EyePupilDiaMeter;
    vec3 eyeCenter = rec_config.EyeCenter;


    Real* dimg = new Real[N];
    memset(dimg, 0.0, sizeof(Real) * N);

    Real maxvalue = src[0].mag();
    for (int k = 0; k < N; k++)
    {
        Real val = src[k].mag();
        maxvalue = val > maxvalue ? val : maxvalue;
        dimg[k] = val;
    }

    Real SAT_VAL = maxvalue * ratioAtPupil;
    Real hss_x = (pnx * ppx) / 2.0;
    Real hss_y = (pny * ppy) / 2.0;
    Real halfPupil = eyePupil / 2.0;

    Real maxv = dimg[0], minv = dimg[0];
    for (int k = 0; k < N; k++)
    {
        if (dimg[k] > SAT_VAL)
            dimg[k] = SAT_VAL;

        maxv = (dimg[k] > maxv) ? dimg[k] : maxv;
        minv = (dimg[k] < minv) ? dimg[k] : minv;
    }

    for (int k = 0; k < N; k++)
    {
        int x = k % pnx;
        int y = k / pnx;

        Real xx = -hss_x + (ppx * x);
        Real yy = -hss_y + (pny - 1) * ppy - (ppy * y);
        Real xxx = xx - eyeCenter[_X];
        Real yyy = yy - eyeCenter[_Y];
        bool eye_pupil_mask = sqrt(xxx * xxx + yyy * yyy) < halfPupil ? 1.0 : 0.0;

        Real val = dimg[k];
        Real field_out = (val - minv) / (maxv - minv) * 255.0;
        Real field_in = (val - minv) / (maxv - minv) * 127.0 + 128.0;
        dimg[k] = field_in * eye_pupil_mask + field_out * (1 - eye_pupil_mask);
        //dimg[k] = field_in * eye_pupil_mask;

    }
    ScaleBilnear(dimg, dst, pnx, pny, scaleX, scaleY);

    delete[] dimg;
}

void ophRec::getVarname(int vtr, vec3& var_vals, std::string& varname2)
{
    bool bSimPos[3];
    memcpy(&bSimPos[0], rec_config.SimulationPos, sizeof(bSimPos));

    std::string varname;
    varname.clear();
    varname2.clear();
    if (rec_config.SimulationMode == 0) {

        varname.append("FOCUS");

        LOG("Step # %d %s = %.8f \n", vtr + 1, varname.c_str(), var_vals[0]);
        char temp[100];
        sprintf(temp, "%.5f", var_vals[0]);
        varname2.clear();
        varname2.append(varname).append("_").append(temp);
        varname2.replace(varname2.find('.'), 1, "_");

    }
    else {

        varname.append("POSITION");

        if (bSimPos[_X]) varname.append("_X");
        if (bSimPos[_Y]) varname.append("_Y");
        if (bSimPos[_Z]) varname.append("_Z");

        LOG("Step # %d %s = ", vtr + 1, varname.c_str());
        varname2.clear();
        varname2.append(varname);

        if (bSimPos[_X]) {
            LOG("%.8f ", var_vals[0]);
            char temp[100];
            sprintf(temp, "%.5f", var_vals[0]);
            varname2.append("_").append(temp);
            varname2.replace(varname2.find('.'), 1, "_");
        }
        if (bSimPos[_Y]) {
            LOG("%.8f ", var_vals[1]);
            char temp[100];
            sprintf(temp, "%.5f", var_vals[1]);
            varname2.append("_").append(temp);
            varname2.replace(varname2.find('.'), 1, "_");
        }
        if (bSimPos[_Z]) {
            LOG("%.8f ", var_vals[2]);
            char temp[100];
            sprintf(temp, "%.5f", var_vals[2]);
            varname2.append("_").append(temp);
            varname2.replace(varname2.find('.'), 1, "_");
        }
        LOG("\n");
    }
}

void ophRec::Clear()
{
    for (vector<Real*>::iterator it = m_vecEncoded.begin(); it != m_vecEncoded.end(); it++)
    {
        delete[](*it);
    }

    for (vector<uchar*>::iterator it = m_vecNormalized.begin(); it != m_vecNormalized.end(); it++)
    {
        delete[](*it);
    }
    m_vecEncoded.clear();
    m_vecNormalized.clear();
}

bool ophRec::ReconstructImage()
{

    Clear();
    auto begin = CUR_TIME;

    LOG("1) Algorithm Method : Angular Spectrum\n");
    LOG("2) Reconstruct Image with %s\n", m_mode & MODE_GPU ?
        "GPU" :
#ifdef _OPENMP
        "Multi Core CPU"
#else
        "Single Core CPU"
#endif
    );

    m_mode & MODE_GPU ? ASM_Propagation_GPU() : ASM_Propagation();
    
    LOG("Total Elapsed Time: %lf (s)\n", ELAPSED_TIME(begin, CUR_TIME));
    return true;
}

void ophRec::Initialize()
{
    const int nChannel = context_.waveNum;
    const int N = context_.pixel_number[_X] * context_.pixel_number[_Y];

    // Memory Location for Result Image
    if (complex_H != nullptr) {
        for (int i = 0; i < m_nOldChannel; i++) {
            if (complex_H[i] != nullptr) {
                delete[] complex_H[i];
                complex_H[i] = nullptr;
            }
        }
        delete[] complex_H;
        complex_H = nullptr;
    }
    complex_H = new Complex<Real>*[nChannel];
    for (int i = 0; i < nChannel; i++) {
        complex_H[i] = new Complex<Real>[N];
        memset(complex_H[i], 0, sizeof(Complex<Real>) * N);
    }
    m_nOldChannel = nChannel;
}

void ophRec::ophFree(void)
{
    Openholo::ophFree();

    for (vector<Real*>::iterator it = m_vecEncoded.begin(); it != m_vecEncoded.end(); it++)
    {
        delete (*it);
    }
    m_vecEncoded.clear();

    for (vector<uchar*>::iterator it = m_vecNormalized.begin(); it != m_vecNormalized.end(); it++)
    {
        delete (*it);
    }
    m_vecNormalized.clear();
}

void circshift(Real* in, Real* out, int shift_x, int shift_y, int nx, int ny)
{
    int ti, tj;
    for (int i = 0; i < nx; i++)
    {
        for (int j = 0; j < ny; j++)
        {
            ti = (i + shift_x) % nx;
            if (ti < 0)
                ti = ti + nx;
            tj = (j + shift_y) % ny;
            if (tj < 0)
                tj = tj + ny;

            out[ti + tj * nx] = in[i + j * nx];
        }
    }
}

void circshift(Complex<Real>* in, Complex<Real>* out, int shift_x, int shift_y, int nx, int ny)
{
    int ti, tj;
    for (int i = 0; i < nx; i++)
    {
        for (int j = 0; j < ny; j++)
        {
            ti = (i + shift_x) % nx;
            if (ti < 0)
                ti = ti + nx;
            tj = (j + shift_y) % ny;
            if (tj < 0)
                tj = tj + ny;

            out[ti + tj * nx] = in[i + j * nx];
        }
    }
}

vec3 image_sample(float xx, float yy, int c, size_t w, size_t h, double* in)
{
    int x1 = (int)floor(xx);
    int x2 = (int)ceil(xx);
    int y1 = (int)floor(yy);
    int y2 = (int)ceil(yy);

    if (x1 < 0 || x1 >= (int)w || x2 < 0 || x2 >= (int)w) return vec3(0);
    if (y1 < 0 || y1 >= (int)h || y2 < 0 || y2 >= (int)h) return vec3(0);

    vec3 ret(0);
    double v1, v2, v3, v4, tvx, tvy;

    tvx = xx - floor(xx);
    tvy = yy - floor(yy);
    int tc = min(c, 3);
    for (int i = 0; i < tc; i++) {
        v1 = IMAGE_VAL(x1, y1, i, w, c, in);
        v2 = IMAGE_VAL(x2, y1, i, w, c, in);
        v3 = IMAGE_VAL(x1, y2, i, w, c, in);
        v4 = IMAGE_VAL(x2, y2, i, w, c, in);
        v1 = (1.0 - tvx)*v1 + tvx * v2;
        v3 = (1.0 - tvx)*v3 + tvx * v4;
        v1 = (1.0 - tvy)*v1 + tvy * v3;

        ret[i] = v1;
    }

    return ret;
}

void ScaleBilnear(double* src, double* dst, int w, int h, int neww, int newh, double multiplyval)
{
    for (int y = 0; y < newh; y++)
    {
        for (int x = 0; x < neww; x++)
        {
            float gx = (x / (float)neww) * (w - 1);
            float gy = (y / (float)newh) * (h - 1);

            vec3 ret = multiplyval * image_sample(gx, gy, 1, w, h, src);
            dst[x + y * neww] = ret[0];

            /*
            int gxi = (int)gx;
            int gyi = (int)gy;

            double a00 = src[gxi + 0 + gyi * w];
            double a01 = src[gxi + 1 + gyi * w];
            double a10 = src[gxi + 0 + (gyi + 1)*w];
            double a11 = src[gxi + 1 + (gyi + 1)*w];

            float dx = gx - gxi;
            float dy = gy - gyi;

            dst[x + y * neww] = multiplyval * (a00 * (1 - dx)*(1 - dy) + a01 * dx*(1 - dy) + a10 * (1 - dx)*dy + a11 * dx*dy);
            */

        }
    }
}



void rotateCCW180(double* src, double* dst, int pnx, int pny, double mulival)
{
    for (int i = 0; i < pnx*pny; i++)
    {
        int x = i % pnx;
        int y = i / pnx;

        int newx = pnx - x - 1;
        int newy = pny - y - 1;

        dst[newx + newy * pnx] = mulival * src[x + y * pnx];

    }

}

void reArrangeChannel(std::vector<double*>& src, double* dst, int pnx, int pny, int chnum)
{
    for (int k = 0; k < pnx*pny; k++)
    {
        for (int c = 0; c < chnum; c++)
        {
            if (c == 0)
                dst[k*chnum + 2] = src[c][k];
            else if (c == 2)
                dst[k*chnum + 0] = src[c][k];
            else
                dst[k*chnum + c] = src[c][k];
        }

    }
}