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#include "SMCalibrationWorker.h"
#include "SMCalibrationParameters.h"

#include "cvtools.h"

#include <opencv2/aruco/charuco.hpp>

#include <QSettings>
#include <QTextStream>

#include <ceres/ceres.h>

// Closed form solution to solve for the rotation axis from sets of 3D point coordinates of flat pattern feature points
// Algorithm according to Chen et al., Rotation axis calibration of a turntable using constrained global optimization, Optik 2014
// DTU, 2014, Jakob Wilm
static void rotationAxisEstimation(const std::vector< std::vector<cv::Point3f> > Qcam,
                                   const std::vector<cv::Point3f> Qobj,
                                   cv::Vec3f &axis, cv::Vec3f &point){
    assert(Qobj.size() == Qcam[0].size());

    // number of frames (points on each arch)
    auto l = Qcam.size();

    // number of points in each frame
    size_t mn = Qobj.size();

    // construct matrix for axis determination
    cv::Mat M(6, 6, CV_32F, cv::Scalar(0));

    for(int k=0; k<l; k++){
        for(unsigned int idx=0; idx<mn; idx++){

            //            float i = Qobj[idx].x+4;
            //            float j = Qobj[idx].y+4;
            float i = Qobj[idx].x;
            float j = Qobj[idx].y;

            float x = Qcam[k][idx].x;
            float y = Qcam[k][idx].y;
            float z = Qcam[k][idx].z;

            M += (cv::Mat_<float>(6,6) << x*x, x*y, x*z, x, i*x, j*x,
                  0, y*y, y*z, y, i*y, j*y,
                  0,   0, z*z, z, i*z, j*z,
                  0,   0,   0, 1,   i,   j,
                  0,   0,   0, 0, i*i, i*j,
                  0,   0,   0, 0,   0, j*j);

        }
    }

    cv::completeSymm(M, false);

    // solve for axis
    std::vector<float> lambda;
    cv::Mat u;
    cv::eigen(M, lambda, u);

    float minLambda = std::abs(lambda[0]);
    int idx = 0;
    for(unsigned int i=1; i<lambda.size(); i++){
        if(abs(lambda[i]) < minLambda){
            minLambda = lambda[i];
            idx = i;
        }
    }

    axis = u.row(idx).colRange(0, 3);
    axis = cv::normalize(axis);

    float nx = u.at<float>(idx, 0);
    float ny = u.at<float>(idx, 1);
    float nz = u.at<float>(idx, 2);
    //float d  = u.at<float>(idx, 3);
    float dh = u.at<float>(idx, 4);
    float dv = u.at<float>(idx, 5);

    // Paper version: c is initially eliminated
    /*cv::Mat A(l*mn, mn+2, CV_32F, cv::Scalar(0.0));
        cv::Mat bb(l*mn, 1, CV_32F);

        for(int k=0; k<l; k++){
            for(unsigned int idx=0; idx<mn; idx++){

                float i = Qobj[idx].x;
                float j = Qobj[idx].y;

                float x = Qcam[k][idx].x;
                float y = Qcam[k][idx].y;
                float z = Qcam[k][idx].z;

                float f = x*x + y*y + z*z + (2*x*nx + 2*y*ny + 2*z*nz)*(i*dh + j*dv);

                int row = k*mn+idx;
                A.at<float>(row, 0) = 2*x - (2*z*nx)/nz;
                A.at<float>(row, 1) = 2*y - (2*z*ny)/nz;
                A.at<float>(row, idx+2) = 1.0;

                bb.at<float>(row, 0) = f + (2*z*d)/nz;
            }
        }

        // solve for point
        cv::Mat abe;
        cv::solve(A, bb, abe, cv::DECOMP_SVD);

        float a = abe.at<float>(0, 0);
        float b = abe.at<float>(1, 0);
        float c = -(nx*a+ny*b+d)/nz;
        */

    // Our version: solve simultanously for a,b,c
    cv::Mat A(l*mn, mn+3, CV_32F, cv::Scalar(0.0));
    cv::Mat bb(l*mn, 1, CV_32F);

    for(int k=0; k<l; k++){
        for(unsigned int idx=0; idx<mn; idx++){

            float i = Qobj[idx].x;
            float j = Qobj[idx].y;

            float x = Qcam[k][idx].x;
            float y = Qcam[k][idx].y;
            float z = Qcam[k][idx].z;

            float f = x*x + y*y + z*z + (2*x*nx + 2*y*ny + 2*z*nz)*(i*dh + j*dv);

            int row = k*mn+idx;
            A.at<float>(row, 0) = 2*x;
            A.at<float>(row, 1) = 2*y;
            A.at<float>(row, 2) = 2*z;
            A.at<float>(row, idx+3) = 1.0;

            bb.at<float>(row, 0) = f;
        }
    }

    // solve for point
    cv::Mat abe;
    cv::solve(A, bb, abe, cv::DECOMP_SVD);

    float a = abe.at<float>(0, 0);
    float b = abe.at<float>(1, 0);
    float c = abe.at<float>(2, 0);

    point[0] = a;
    point[1] = b;
    point[2] = c;

}

struct CircleResidual {
    CircleResidual(std::vector<cv::Point3f> _pointsOnArc)
        : pointsOnArc(_pointsOnArc) {}

    template <typename T>
    bool operator()(const T* point, const T* axis, T* residual) const {

        T axisSqNorm = axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2];

        unsigned int l = pointsOnArc.size();
        std::vector<T> dI(l);

        // note, this is automatically initialized to 0
        T sum(0.0);

        for(unsigned int i=0; i<l; i++){
            cv::Point3d p = pointsOnArc[i];
            //T p[3] = {pointsOnArc[i].x, pointsOnArc[i].y, pointsOnArc[i].z};

            // point to line distance
            T dotProd = (point[0]-p.x)*axis[0] + (point[1]-p.y)*axis[1] + (point[2]-p.z)*axis[2];
            T dIx = point[0] - p.x - (dotProd*axis[0]/axisSqNorm);
            T dIy = point[1] - p.y - (dotProd*axis[1]/axisSqNorm);
            T dIz = point[2] - p.z - (dotProd*axis[2]/axisSqNorm);
            dI[i] = ceres::sqrt(dIx*dIx + dIy*dIy + dIz*dIz);

            sum += dI[i];
        }

        T mean = sum / double(l);

        for(unsigned int i=0; i<l; i++){
            residual[i] = dI[i] - mean;
        }

        return true;
    }

    private:
        // Observations for one checkerboard corner.
        const std::vector<cv::Point3f> pointsOnArc;
};

static void rotationAxisOptimization(const std::vector< std::vector<cv::Point3f> > Qcam, const std::vector<cv::Point3f> Qobj, cv::Vec3f &axis, cv::Vec3f &point, float &error){

    // number of frames (points on each arch)
    size_t l = Qcam.size();

    // number of points in each frame
    size_t mn = Qobj.size();

    // read initial guess
    double pointArray[] = {point[0], point[1], point[2]};
    double axisArray[] = {axis[0], axis[1], axis[2]};

    ceres::Problem problem;

    // loop through saddle points
    for(unsigned int idx=0; idx<mn; idx++){
        std::vector<cv::Point3f> pointsOnArch(l);
        for(unsigned int k=0; k<l; k++){
            pointsOnArch[k] = Qcam[k][idx];
        }
        ceres::CostFunction* cost_function =
                new ceres::AutoDiffCostFunction<CircleResidual, ceres::DYNAMIC, 3, 3>(
                    new CircleResidual(pointsOnArch), l);
        problem.AddResidualBlock(cost_function, NULL, pointArray, axisArray);
    }

    // Run the solver!
    ceres::Solver::Options options;
    options.linear_solver_type = ceres::DENSE_QR;
    options.minimizer_progress_to_stdout = true;
    ceres::Solver::Summary summary;
    ceres::Solve(options, &problem, &summary);

    std::cout << summary.BriefReport() << "\n";

    point = cv::Vec3f(pointArray[0], pointArray[1], pointArray[2]);
    axis = cv::Vec3f(axisArray[0], axisArray[1], axisArray[2]);
    axis /= cv::norm(axis);


    // Error estimate (sum of squared differences)
    error = 0;
    // loop through saddle points
    for(unsigned int idx=0; idx<mn; idx++){

        // vector of distances from rotation axis
        std::vector<float> dI(l);
        // loop through angular positions
        for(unsigned int k=0; k<l; k++){
            cv::Vec3f p = cv::Vec3f(Qcam[k][idx]);
            // point to line distance
            dI[k] = cv::norm((point-p)-(point-p).dot(axis)*axis);
        }
        float sum = std::accumulate(dI.begin(), dI.end(), 0.0);
        float mean = sum / dI.size();
        float meanDev = 0;
        for(unsigned int k=0; k<l; k++){
            meanDev += std::abs(dI[k] - mean);
        }
        meanDev /= l;
        error += meanDev;
    }
    error /= mn;
}

static std::vector<cv::Point3f> generateWorldCoords(const cv::Size checkerCount, const float checkerSize){

    std::vector<cv::Point3f> Qi;
    for (int h=0; h<checkerCount.height; h++)
        for (int w=0; w<checkerCount.width; w++)
            Qi.push_back(cv::Point3f(checkerSize * w, checkerSize* h, 0.0));

    return Qi;
}

static bool detectCheckerBoardCorners(const cv::Size & checkerCount,
                                    const cv::Mat & frame,
                                    cv::Mat & frameResult,
                                    std::vector<cv::Point2f> & qc){
    // Convert to grayscale
    cv::Mat gray;
    if(frame.channels() == 1)
        cv::cvtColor(frame, gray, CV_BayerBG2GRAY);
    else
        cv::cvtColor(frame, gray, CV_RGB2GRAY);

    // Extract checker corners
    bool success = cv::findChessboardCorners(gray, checkerCount, qc, cv::CALIB_CB_ADAPTIVE_THRESH + cv::CALIB_CB_FAST_CHECK);
    if(success){
        cv::cornerSubPix(gray, qc, cv::Size(6, 6), cv::Size(1, 1), cv::TermCriteria(CV_TERMCRIT_EPS + CV_TERMCRIT_ITER, 20, 0.0001));
        // Draw colored chessboard
        if(frame.channels() == 1)
            cv::cvtColor(frame, frameResult, CV_BayerBG2RGB);
        else
            frameResult = frame.clone();

        cvtools::drawChessboardCorners(frameResult, checkerCount, qc, success, 10);
    } else {
        qc.clear();
    }
    return success;
}

void SMCalibrationWorker::checkerboardDetection(SMCalibrationSet calibrationSet){

    QSettings settings;
    cv::Size checkerCount(cv::Size(settings.value("calibration/patternSizeX", 22).toInt(), settings.value("calibration/patternSizeY", 13).toInt()));

    bool success0 = detectCheckerBoardCorners(checkerCount, calibrationSet.frame0, calibrationSet.frame0Result, calibrationSet.qc0);
    if(!success0){
//        calibrationSet.qc0.clear();
        emit logMessage(QString("Could not detect checkerboard on set %1 camera0").arg(calibrationSet.id));
        std::cerr << "Could not detect checkerboard on set " << calibrationSet.id << " camera0" << std::endl;
    }

    bool success1 = detectCheckerBoardCorners(checkerCount, calibrationSet.frame1, calibrationSet.frame1Result, calibrationSet.qc1);
    if(!success1){
//        calibrationSet.qc1.clear();
        emit logMessage(QString("Could not detect checkerboard on set %1 camera1").arg(calibrationSet.id));
        std::cerr << "Could not detect checkerboard on set " << calibrationSet.id << " camera1" << std::endl;
    }

    emit newCheckerboardResult(calibrationSet.id, calibrationSet);

}

void SMCalibrationWorker::cameraCalibration(std::vector<SMCalibrationSet> calibrationData){

    QSettings settings;
    cv::Size checkerCount(cv::Size(settings.value("calibration/patternSizeX", 22).toInt(), settings.value("calibration/patternSizeY", 13).toInt()));

    unsigned int nSets = calibrationData.size();

    // 2D Points collected for OpenCV's calibration procedures
    std::vector< std::vector<cv::Point2f> > qc0, qc1, qc0Stereo, qc1Stereo;

    for(unsigned int i=0; i<nSets; i++){

        if(!calibrationData[i].selected)
            continue;

        // Note: avoiding push_back has only minor theoretical value
        if(!calibrationData[i].qc0.empty())
            qc0.push_back(calibrationData[i].qc0);

        if(!calibrationData[i].qc1.empty())
            qc1.push_back(calibrationData[i].qc1);

        if(!calibrationData[i].qc0.empty() && !calibrationData[i].qc1.empty()){
            qc0Stereo.push_back(calibrationData[i].qc0);
            qc1Stereo.push_back(calibrationData[i].qc1);
        }
    }

    // Generate world object coordinates [mm]
    std::vector<cv::Point3f> Qi = generateWorldCoords(checkerCount, settings.value("calibration/squareSize", 10.0).toFloat());

    std::vector< std::vector<cv::Point3f> > Q0(qc0.size(), Qi), Q1(qc1.size(), Qi), QStereo(qc0Stereo.size(), Qi);

    // Calibrate the cameras
    SMCalibrationParameters cal;
    cal.frameWidth = calibrationData[0].frame0.cols;
    cal.frameHeight = calibrationData[0].frame0.rows;
    cv::Size frameSize(cal.frameWidth, cal.frameHeight);

    // determine only k1, k2 for lens distortion
    int flags = cv::CALIB_FIX_ASPECT_RATIO + cv::CALIB_FIX_K2 + cv::CALIB_FIX_K3 + cv::CALIB_ZERO_TANGENT_DIST + cv::CALIB_FIX_PRINCIPAL_POINT;

    std::vector<cv::Mat> cam_rvecs0, cam_tvecs0;

    cal.cam0_error = cv::calibrateCamera(Q0, qc0, frameSize, cal.K0, cal.k0, cam_rvecs0, cam_tvecs0, cal.cam0_intrinsic_std, cal.cam0_extrinsic_std, cal.cam0_errors_per_view, flags,
                                         cv::TermCriteria(cv::TermCriteria::COUNT+cv::TermCriteria::EPS, 100, DBL_EPSILON));

    std::vector<cv::Mat> cam_rvecs1, cam_tvecs1;
    cal.cam1_error = cv::calibrateCamera(Q1, qc1, frameSize, cal.K1, cal.k1, cam_rvecs1, cam_tvecs1, cal.cam1_intrinsic_std, cal.cam1_extrinsic_std, cal.cam1_errors_per_view, flags,
                                         cv::TermCriteria(cv::TermCriteria::COUNT+cv::TermCriteria::EPS, 100, DBL_EPSILON));

    // Stereo calibration
    int flags_stereo = cv::CALIB_FIX_INTRINSIC;// + cv::CALIB_FIX_K2 + cv::CALIB_FIX_K3 + cv::CALIB_ZERO_TANGENT_DIST + cv::CALIB_FIX_PRINCIPAL_POINT + cv::CALIB_FIX_ASPECT_RATIO;
    cv::Mat E, F, R1, T1;

    #if CV_MAJOR_VERSION < 3
        cal.stereo_error = cv::stereoCalibrate(QStereo, qc0Stereo, qc1Stereo, cal.K0, cal.k0, cal.K1, cal.k1,
                                               frameSize, R1, T1, E, F,
                                               cv::TermCriteria(cv::TermCriteria::COUNT + cv::TermCriteria::EPS, 200, DBL_EPSILON),
                                               flags_stereo);
    #else
        cal.stereo_error = cv::stereoCalibrate(QStereo, qc0Stereo, qc1Stereo, cal.K0, cal.k0, cal.K1, cal.k1,
                                               frameSize, R1, T1, E, F, flags_stereo,
                                               cv::TermCriteria(cv::TermCriteria::COUNT + cv::TermCriteria::EPS, 200, DBL_EPSILON));
    #endif

    cal.R1 = R1;
    cal.T1 = T1;
    cal.E = E;
    cal.F = F;

    // Print to log
    std::stringstream out;
    out << "## Camera Calibration ##" << std::endl
        << "No. images used for intrinsics of cam0: " << qc0.size() << std::endl
        << "No. images used for intrinsics of cam1: " << qc1.size() << std::endl
        << "No. images used for stereo calibration: " << qc0Stereo.size() << std::endl;
    cal.printCamera(out);
    out << std::endl << std::endl;
    emit logMessage(QString::fromStdString(out.str()));

    // save to (reentrant) qsettings object
    settings.setValue("calibration/parameters", QVariant::fromValue(cal));

    emit done();
}

static void drawDetectedMarkersCharuco(cv::InputOutputArray _image, cv::InputArrayOfArrays _corners,
                                cv::InputArray _ids, cv::Scalar borderColor) {

    using namespace cv;
    using namespace std;

    CV_Assert(_image.getMat().total() != 0 &&
              (_image.getMat().channels() == 1 || _image.getMat().channels() == 3));
    CV_Assert((_corners.total() == _ids.total()) || _ids.total() == 0);

    // calculate colors
    Scalar textColor, cornerColor;
    textColor = cornerColor = borderColor;
    swap(textColor.val[0], textColor.val[1]);     // text color just sawp G and R
    swap(cornerColor.val[1], cornerColor.val[2]); // corner color just sawp G and B

    int nMarkers = (int)_corners.total();
    for(int i = 0; i < nMarkers; i++) {
        Mat currentMarker = _corners.getMat(i);
        CV_Assert(currentMarker.total() == 4 && currentMarker.type() == CV_32FC2);

        // draw marker sides
        for(int j = 0; j < 4; j++) {
            Point2f p0, p1;
            p0 = currentMarker.ptr< Point2f >(0)[j];
            p1 = currentMarker.ptr< Point2f >(0)[(j + 1) % 4];
            line(_image, p0, p1, borderColor, 2, LINE_AA);
        }
        // draw first corner mark
        rectangle(_image, currentMarker.ptr< Point2f >(0)[0] - Point2f(3, 3),
                  currentMarker.ptr< Point2f >(0)[0] + Point2f(3, 3), cornerColor, 1, LINE_AA);

        // draw ID
        if(_ids.total() != 0) {
            Point2f cent(0, 0);
            for(int p = 0; p < 4; p++)
                cent += currentMarker.ptr< Point2f >(0)[p];
            cent = cent / 4.;
            stringstream s;
            s << _ids.getMat().ptr< int >(0)[i];
            putText(_image, s.str(), cent, FONT_HERSHEY_SIMPLEX, 1, textColor, 2, LINE_AA);
        }
    }
}

static void drawDetectedCornersCharuco(cv::InputOutputArray _image, cv::InputArray _charucoCorners,
                                       cv::InputArray _charucoIds, cv::Scalar cornerColor) {

    using namespace cv;
    using namespace std;

    CV_Assert(_image.getMat().total() != 0 &&
              (_image.getMat().channels() == 1 || _image.getMat().channels() == 3));
    CV_Assert((_charucoCorners.getMat().total() == _charucoIds.getMat().total()) ||
              _charucoIds.getMat().total() == 0);

    unsigned int nCorners = (unsigned int)_charucoCorners.getMat().total();
    for(unsigned int i = 0; i < nCorners; i++) {
        Point2f corner = _charucoCorners.getMat().at< Point2f >(i);

        // draw first corner mark
        rectangle(_image, corner - Point2f(3, 3), corner + Point2f(3, 3), cornerColor, 2, LINE_AA);

        // draw ID
        if(_charucoIds.total() != 0) {
            int id = _charucoIds.getMat().at< int >(i);
            stringstream s;
            s << id;
            putText(_image, s.str(), corner + Point2f(5, -5), FONT_HERSHEY_SIMPLEX, 1.0,
                    cornerColor, 4, cv::LINE_AA);
        }
    }
}


static bool detectCheckerBoardCornersCharuco(const cv::Mat & frame,
                                            const cv::Ptr<cv::aruco::Dictionary> dict,
                                            const cv::Ptr<cv::aruco::CharucoBoard> board,
                                            const cv::Ptr<cv::aruco::DetectorParameters> parameters,
                                            cv::Mat& frameResult,
                                            std::vector<cv::Point2f>& qc,
                                            std::vector<int>& qci){

    // Convert to grayscale
    cv::Mat gray;
    if(frame.channels() == 1)
        cv::cvtColor(frame, gray, CV_BayerBG2GRAY);
    else
        cv::cvtColor(frame, gray, CV_RGB2GRAY);


    std::vector<std::vector<cv::Point2f>> mc;
    std::vector<int> mi;

    cv::Mat grayBlurred;
    cv::GaussianBlur(gray, grayBlurred, cv::Size(0, 0), 3);

    // Extract checker corners
    cv::aruco::detectMarkers(grayBlurred, dict, mc, mi, parameters);
    //std::vector<std::vector<cv::Point2f>> mc, rejecti;
    //cv::aruco::refineDetectedMarkers(gray0, board, mc0, mi0, rejecti0);

    //cv::Mat cci, cidsi;
    cv::aruco::interpolateCornersCharuco(mc, mi, gray, board, qc, qci, cv::noArray(), cv::noArray(), 1);

    bool success = (qc.size() >= 4);
    if(success){
        cv::cornerSubPix(gray, qc, cv::Size(6, 6), cv::Size(1, 1), cv::TermCriteria(CV_TERMCRIT_EPS + CV_TERMCRIT_ITER, 20, 0.0001));
        // Draw colored chessboard
        if(frame.channels() == 1)
            cv::cvtColor(frame, frameResult, CV_BayerBG2RGB);
        else
            frameResult = frame.clone();

        // Draw colored chessboard
        drawDetectedMarkersCharuco(frameResult, mc, mi, cv::Scalar(0, 255, 0));
        drawDetectedCornersCharuco(frameResult, qc, qci, cv::Scalar(0, 255, 0));
    } else {
        qc.clear();
    }

    return success;

}

void SMCalibrationWorker::checkerboardDetectionCharuco(SMCalibrationSet calibrationSet){

    QSettings settings;
    cv::Size checkerCount(cv::Size(settings.value("calibration/patternSizeX", 22).toInt(), settings.value("calibration/patternSizeY", 13).toInt()));
    const float checkerSize = settings.value("calibration/squareSize", 10.0).toFloat();
    float markerLength = 0.8f*checkerSize;

    // Charuco board and dictionary
    cv::Ptr<cv::aruco::Dictionary> dict = cv::aruco::getPredefinedDictionary(cv::aruco::DICT_6X6_250);
    cv::Ptr<cv::aruco::CharucoBoard> board = cv::aruco::CharucoBoard::create(checkerCount.width+1, checkerCount.height+1, checkerSize, markerLength, dict);

    //    cv::Mat boardImg;
    //    board->draw(cv::Size((saddlePointCountX+1)*100, (saddlePointCountY+1)*100), boardImg, 0, 1);
    //    cv::Mat boardImgRes;
    //    cv::resize(boardImg, boardImgRes, cv::Size((saddlePointCountX+1)*10, (saddlePointCountY+1)*10), 0, 0, cv::INTER_NEAREST);
    //    cv::imwrite("boardImg.png", boardImg);
    //    cv::imwrite("boardImgRes.png", boardImgRes);

    cv::Ptr<cv::aruco::DetectorParameters> parameters = cv::aruco::DetectorParameters::create();
//    parameters->adaptiveThreshWinSizeMin = 3;
//    parameters->adaptiveThreshWinSizeMax = 153;
//    parameters->adaptiveThreshWinSizeStep = 5;
//    parameters->adaptiveThreshConstant = 20;
//    parameters->minMarkerPerimeterRate = 0.01;
    parameters->maxMarkerPerimeterRate = 5.0;
//    parameters->minCornerDistanceRate = 0.10;
//    parameters->perspectiveRemovePixelPerCell = 6;
//    parameters->maxErroneousBitsInBorderRate = 0.8;
//    parameters->minOtsuStdDev = 1;
//    parameters->errorCorrectionRate = 0.1;
    parameters->cornerRefinementWinSize = 10;

    bool success0 = detectCheckerBoardCornersCharuco(calibrationSet.frame0, dict, board, parameters, calibrationSet.frame0Result, calibrationSet.qc0, calibrationSet.qc0id);
    if(!success0){
        emit logMessage(QString("Could not detect  Charuco corners on set %1 camera0").arg(calibrationSet.id));
        std::cerr << "Could not detect Charuco corners on set " << calibrationSet.id << " camera0" << std::endl;
    }

    bool success1 = detectCheckerBoardCornersCharuco(calibrationSet.frame1, dict, board, parameters, calibrationSet.frame1Result, calibrationSet.qc1, calibrationSet.qc1id);
    if(!success1){
        emit logMessage(QString("Could not detect Charuco corners on set %1 camera1").arg(calibrationSet.id));
        std::cerr << "Could not detect Charuco corners on set " << calibrationSet.id << " camera1" << std::endl;
    }

    emit newCheckerboardResult(calibrationSet.id, calibrationSet);

}

void SMCalibrationWorker::cameraCalibrationCharuco(std::vector<SMCalibrationSet> calibrationData){

    QSettings settings;

    // Number of saddle points on calibration pattern
    cv::Size checkerCount(cv::Size(settings.value("calibration/patternSizeX", 22).toInt(), settings.value("calibration/patternSizeY", 13).toInt()));
    const float checkerSize = settings.value("calibration/squareSize", 10.0).toFloat();
    float markerLength = 0.8f*checkerSize;

    cv::Ptr<cv::aruco::Dictionary> dict = cv::aruco::getPredefinedDictionary(cv::aruco::DICT_6X6_250);
    cv::Ptr<cv::aruco::CharucoBoard> board = cv::aruco::CharucoBoard::create(checkerCount.width+1, checkerCount.height+1, checkerSize, markerLength, dict);

    auto nSets = calibrationData.size();

    // 2D Points collected for OpenCV's calibration procedures
    std::vector< std::vector<cv::Point2f> > qc0, qc1;
    std::vector< std::vector<cv::Point2f> > qc0Stereo, qc1Stereo;

    // 3D object points
    std::vector< std::vector<cv::Point3f> > Q0, Q1, QStereo;

    // Loop through calibration sets
    for(unsigned int i=0; i<nSets; i++){

        if(!calibrationData[i].selected)
            continue;

        bool success0 = !calibrationData[i].qc0.empty();
        bool success1 = !calibrationData[i].qc1.empty();

        if(success0){
            std::vector<cv::Point3f> Q0i;
            for(std::size_t j=0; j<calibrationData[i].qc0id.size(); j++){
                int id = calibrationData[i].qc0id[j];
                Q0i.push_back(board->chessboardCorners[id]);
            }

            qc0.push_back(calibrationData[i].qc0);
            Q0.push_back(Q0i);
        }

        if(success1){
            std::vector<cv::Point3f> Q1i;
            for(std::size_t j=0; j<calibrationData[i].qc1id.size(); j++){
                int id = calibrationData[i].qc1id[j];
                Q1i.push_back(board->chessboardCorners[id]);
            }

            qc1.push_back(calibrationData[i].qc1);
            Q1.push_back(Q1i);
        }

        if(success0 && success1){

            std::vector<cv::Point2f> qc0iStereo, qc1iStereo;
            std::vector<cv::Point3f> QiStereo;

            int j0 = 0;
            int j1 = 0;
            while(j0<calibrationData[i].qc0.size() && j1<calibrationData[i].qc1.size()){

                int id0 = calibrationData[i].qc0id[j0];
                int id1 = calibrationData[i].qc1id[j1];

                if(id0 < id1)
                    j0++;
                else if (id1 < id0)
                    j1++;
                else{
                    assert(id0 == id1);
                    qc0iStereo.push_back(calibrationData[i].qc0[j0]);
                    qc1iStereo.push_back(calibrationData[i].qc1[j1]);
                    QiStereo.push_back(board->chessboardCorners[id0]);
                    j0++;
                    j1++;
                }

            }

            if(QiStereo.size() > 0){
                qc0Stereo.push_back(qc0iStereo);
                qc1Stereo.push_back(qc1iStereo);
                QStereo.push_back(QiStereo);
            }
        }

    }

    size_t nValidSets = qc0Stereo.size();
    if(nValidSets < 2){
        std::cerr << "Not enough valid calibration sequences!" << std::endl;
        emit done();
        return;
    }


    // calibrate the cameras
    SMCalibrationParameters cal;
    cal.frameWidth = calibrationData[0].frame0.cols;
    cal.frameHeight = calibrationData[0].frame0.rows;
    cv::Size frameSize(cal.frameWidth, cal.frameHeight);

    // determine only k1, k2 for lens distortion
    int flags = cv::CALIB_FIX_ASPECT_RATIO + cv::CALIB_FIX_K3 + cv::CALIB_ZERO_TANGENT_DIST + cv::CALIB_FIX_PRINCIPAL_POINT;

    // Note: several of the output arguments below must be cv::Mat, otherwise segfault
    std::vector<cv::Mat> cam_rvecs0, cam_tvecs0;
    cal.cam0_error = cv::calibrateCamera(Q0, qc0, frameSize, cal.K0, cal.k0, cam_rvecs0, cam_tvecs0, cal.cam0_intrinsic_std, cal.cam0_extrinsic_std, cal.cam0_errors_per_view, flags,
                                         cv::TermCriteria(cv::TermCriteria::COUNT+cv::TermCriteria::EPS, 100, DBL_EPSILON));

    std::vector<cv::Mat> cam_rvecs1, cam_tvecs1;
    cal.cam1_error = cv::calibrateCamera(Q1, qc1, frameSize, cal.K1, cal.k1, cam_rvecs1, cam_tvecs1, cal.cam1_intrinsic_std, cal.cam1_extrinsic_std, cal.cam1_errors_per_view, flags,
                                         cv::TermCriteria(cv::TermCriteria::COUNT+cv::TermCriteria::EPS, 100, DBL_EPSILON));

    // stereo calibration
    int flags_stereo = cv::CALIB_FIX_INTRINSIC;// + cv::CALIB_FIX_K2 + cv::CALIB_FIX_K3 + cv::CALIB_ZERO_TANGENT_DIST + cv::CALIB_FIX_PRINCIPAL_POINT + cv::CALIB_FIX_ASPECT_RATIO;
    cv::Mat E, F, R1, T1;

    #if CV_MAJOR_VERSION < 3
        cal.stereo_error = cv::stereoCalibrate(QStereo, qc0Stereo, qc1Stereo, cal.K0, cal.k0, cal.K1, cal.k1,
                                               frameSize, R1, T1, E, F,
                                               cv::TermCriteria(cv::TermCriteria::COUNT + cv::TermCriteria::EPS, 200, DBL_EPSILON),
                                               flags_stereo);
    #else
        cal.stereo_error = cv::stereoCalibrate(QStereo, qc0Stereo, qc1Stereo, cal.K0, cal.k0, cal.K1, cal.k1,
                                               frameSize, R1, T1, E, F, flags_stereo,
                                               cv::TermCriteria(cv::TermCriteria::COUNT + cv::TermCriteria::EPS, 200, DBL_EPSILON));
    #endif

    cal.R1 = R1;
    cal.T1 = T1;
    cal.E = E;
    cal.F = F;

    // Print to log
    std::stringstream out;
    out << "## Camera Calibration ##" << std::endl
        << "No. images used for intrinsics of cam0: " << qc0.size() << std::endl
        << "No. images used for intrinsics of cam1: " << qc1.size() << std::endl
        << "No. images used for stereo calibration: " << qc0Stereo.size() << std::endl;
    cal.printCamera(out);
    out << std::endl << std::endl;
    emit logMessage(QString::fromStdString(out.str()));

    // save to (reentrant qsettings object)
    settings.setValue("calibration/parameters", QVariant::fromValue(cal));

    emit done();

}


void SMCalibrationWorker::rotationStageCalibration(std::vector<SMCalibrationSet> calibrationData){

    auto nSets = calibrationData.size();

    std::vector< std::vector<cv::Point2f> > qc0Stereo, qc1Stereo;
    std::vector<cv::Point3f> Qi;

    QSettings settings;
    // Generate world object coordinates [mm]
    const cv::Size checkerCount(cv::Size(settings.value("calibration/patternSizeX", 22).toInt(),settings.value("calibration/patternSizeY", 13).toInt()));
    const float checkerSize = settings.value("calibration/squareSize", 10.0).toFloat();

    if(settings.value("calibration/method").toString() == "Charuco"){

        // Find id's which were detected in all images
        std::vector<int> ids;

        for(int i=0; i<calibrationData.size(); i++){

            if(!calibrationData[i].selected)
                continue;

            if(ids.empty()){
                ids = calibrationData[i].qc0id;
            }

            std::vector<int> idsi0;
            std::set_intersection(ids.begin(), ids.end(), calibrationData[i].qc0id.begin(), calibrationData[i].qc0id.end(), std::back_inserter(idsi0));
            ids = idsi0;
            std::vector<int> idsi1;
            std::set_intersection(ids.begin(), ids.end(), calibrationData[i].qc1id.begin(), calibrationData[i].qc1id.end(), std::back_inserter(idsi1));
            ids = idsi1;
        }

        if(ids.size() < 2){
            std::cerr << "Not enough feature points present in all images for rotation axis determination!" << std::endl;
            emit logMessage("Not enough feature points present in all images for rotation axis determination! Deselect some calibration images.");
        }

        for(int i=0; i<calibrationData.size(); i++){

            if(!calibrationData[i].selected)
                continue;

            std::vector<cv::Point2f> qc0StereoI, qc1StereoI;
            for(int j=0; j<ids.size(); j++){

                ptrdiff_t idx0 = std::find(calibrationData[i].qc0id.begin(), calibrationData[i].qc0id.end(), ids[j]) - calibrationData[i].qc0id.begin();
                ptrdiff_t idx1 = std::find(calibrationData[i].qc1id.begin(), calibrationData[i].qc1id.end(), ids[j]) - calibrationData[i].qc1id.begin();

                qc0StereoI.push_back(calibrationData[i].qc0[idx0]);
                qc1StereoI.push_back(calibrationData[i].qc1[idx1]);

            }

            qc0Stereo.push_back(qc0StereoI);
            qc1Stereo.push_back(qc1StereoI);
        }

        float markerLength = 0.8f*checkerSize;

        cv::Ptr<cv::aruco::Dictionary> dict = cv::aruco::getPredefinedDictionary(cv::aruco::DICT_6X6_250);
        cv::Ptr<cv::aruco::CharucoBoard> board = cv::aruco::CharucoBoard::create(checkerCount.width+1, checkerCount.height+1, checkerSize, markerLength, dict);

        for(int j=0; j<ids.size(); j++){
            Qi.push_back(board->chessboardCorners[ids[j]]);
        }

    } else {

        // Normal checkerboard with all corners
        for(auto i=0; i<nSets; i++){

            if(!calibrationData[i].selected)
                continue;

            if(!calibrationData[i].qc0.empty() && !calibrationData[i].qc1.empty()){
                qc0Stereo.push_back(calibrationData[i].qc0);
                qc1Stereo.push_back(calibrationData[i].qc1);
            }
        }

        Qi = generateWorldCoords(checkerCount, checkerSize);

    }

    SMCalibrationParameters cal = settings.value("calibration/parameters").value<SMCalibrationParameters>();

    if(qc0Stereo.size() <= 2){
        std::cerr << "Not enough images for rotation axis determination!" << std::endl;
        emit logMessage("Not enough images for rotation axis determination!");

       cal.Rr = cv::Matx33f::eye();
       cal.Tr = cv::Vec3f(0,0,0);
       cal.rot_axis_error = -1;

       emit done();
       return;
    }

    // Direct rotation axis calibration //
    // full camera matrices
    cv::Matx34f P0 = cv::Matx34f::eye();
    cv::Mat RT1(3, 4, CV_32F);
    cv::Mat(cal.R1).copyTo(RT1(cv::Range(0, 3), cv::Range(0, 3)));
    cv::Mat(cal.T1).copyTo(RT1(cv::Range(0, 3), cv::Range(3, 4)));
    cv::Matx34f P1 = cv::Matx34f(RT1);

    // calibration points in camera 0 frame
    std::vector< std::vector<cv::Point3f> > Qcam(qc0Stereo.size());

    #pragma omp parallel for
    for(unsigned int i=0; i<qc0Stereo.size(); i++){
        std::vector<cv::Point2f> qc0i, qc1i;

        cv::undistortPoints(qc0Stereo[i], qc0i, cal.K0, cal.k0);
        cv::undistortPoints(qc1Stereo[i], qc1i, cal.K1, cal.k1);

        cv::Mat Qhom, Qcami;
        cv::triangulatePoints(P0, P1, qc0i, qc1i, Qhom);
        cvtools::convertMatFromHomogeneous(Qhom, Qcami);
        std::vector<cv::Point3f> QcamiPoints;
        cvtools::matToPoints3f(Qcami, QcamiPoints);

        Qcam[i] = QcamiPoints;
    }

    cv::Vec3f axis, point;
    float rot_axis_error;
    rotationAxisEstimation(Qcam, Qi, axis, point);
    rotationAxisOptimization(Qcam, Qi, axis, point, rot_axis_error);

    // construct transformation matrix
    cv::Vec3f ex = axis.cross(cv::Vec3f(0,0,1.0));
    ex = cv::normalize(ex);
    cv::Vec3f ez = ex.cross(axis);
    ez = cv::normalize(ez);

    cv::Mat RrMat(3, 3, CV_32F);
    cv::Mat(ex).copyTo(RrMat.col(0));
    cv::Mat(axis).copyTo(RrMat.col(1));
    cv::Mat(ez).copyTo(RrMat.col(2));

    cal.Rr = cv::Matx33f(RrMat).t();
    cal.Tr = -cv::Matx33f(RrMat).t()*point;
    cal.rot_axis_error = rot_axis_error;

    // Print to log
    std::stringstream out;
    out << "## Rotation Stage Calibration ##" << std::endl
        << "No. images used for calibration: " << qc0Stereo.size() << std::endl;
    cal.printRotationStage(out);
    out << std::endl << std::endl;
    emit logMessage(QString::fromStdString(out.str()));

    // Save to (reentrant) qsettings object
    settings.setValue("calibration/parameters", QVariant::fromValue(cal));

    emit done();
}