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#include "AlgorithmGrayCode.h"

#include <cmath>

#include "cvtools.h"

#ifndef log2f

#define log2f(x) (log(x)/log(2.0))

#endif

//using namespace std;

/*

 * The purpose of this function is to convert an unsigned

 * binary number to reflected binary Gray code.

 *

 * The operator >> is shift right. The operator ^ is exclusive or.

 * Source: http://en.wikipedia.org/wiki/Gray_code

 */

static unsigned int binaryToGray(unsigned int num) {

    return (num >> 1) ^ num;

}

/*

 * From Wikipedia: http://en.wikipedia.org/wiki/Gray_code

 * The purpose of this function is to convert a reflected binary

 * Gray code number to a binary number.

 */

static unsigned int grayToBinary(unsigned int num){

    unsigned int mask;

    for(mask = num >> 1; mask != 0; mask = mask >> 1)

        num = num ^ mask;

    return num;

}

/*

 * Return the Nth bit of an unsigned integer number

 */

static bool getBit(int decimal, int N){

    return decimal & 1 << (N-1);

}

/*

 * Return the number of bits set in an integer

 */

static int countBits(int n) {

  unsigned int c; // c accumulates the total bits set in v

  for (c = 0; n>0; c++)

    n &= n - 1; // clear the least significant bit set

  return c;

}

/*

 * Return the position of the least significant bit that is set

 */

static int leastSignificantBitSet(int x){

  if(x == 0)

      return 0;

  int val = 1;

  while(x>>=1)

      val++;

  return val;

}

//static int get_bit(int decimal, int N){

//    // Shifting the 1 for N-1 bits

//    int constant = 1 << (N-1);

//    // If the bit is set, return 1

//    if( decimal & constant )

//        return 1;

//    else

//        return 0;

//}

static inline unsigned int powi(int num, unsigned int exponent){

    if(exponent == 0)

        return 1;

    float res = num;

    for(unsigned int i=0; i<exponent-1; i++)

        res *= num;

    return res;

}

static inline unsigned int twopowi(unsigned int exponent){

    return 1 << exponent;

}

// Algorithm

AlgorithmGrayCode::AlgorithmGrayCode(unsigned int _screenCols, unsigned int _screenRows) : Algorithm(_screenCols, _screenRows){

    Nbits = ceilf(log2f((float)screenCols));

    N = 2 + Nbits*2;

    // all on pattern

    cv::Mat allOn(1, screenCols, CV_8UC3, cv::Scalar::all(255));

    patterns.push_back(allOn);

    // all off pattern

    cv::Mat allOff(1, screenCols, CV_8UC3, cv::Scalar::all(0));

    patterns.push_back(allOff);

    // horizontally encoding patterns

    for(unsigned int p=0; p<Nbits; p++){

        cv::Mat pattern(1, screenCols, CV_8UC3);

        cv::Mat patternInv(1, screenCols, CV_8UC3);

        for(unsigned int j=0; j<screenCols; j++){

            unsigned int jGray = binaryToGray(j);

            // Amplitude of channels

            int bit = (int)getBit(jGray, Nbits-p);

            pattern.at<cv::Vec3b>(0,j) = cv::Vec3b(255.0*bit,255.0*bit,255.0*bit);

            int invBit = bit^1;

            patternInv.at<cv::Vec3b>(0,j) = cv::Vec3b(255.0*invBit,255.0*invBit,255.0*invBit);

        }

        patterns.push_back(pattern);

        patterns.push_back(patternInv);

    }

}

cv::Mat AlgorithmGrayCode::getEncodingPattern(unsigned int depth){

    return patterns[depth];

}

bool sortingLarger(cv::Vec4i i,cv::Vec4i j){ return (i[3]<j[3]);}

bool sortingEqual(cv::Vec4i i,cv::Vec4i j){ return (i[3]==j[3]);}

void getEdgeLabels(const cv::Mat& scanLine, int Nbits, std::vector<cv::Vec4i>& edges){

    int nCols = scanLine.cols;

    const int *data = scanLine.ptr<const int>(0);

    int labelLeft;

    int labelRight = data[0];

    // collect edges

    for(int col=1; col<nCols; col++){

        labelLeft = labelRight;

        labelRight = data[col];

        // labels need to be non-background, and differ in exactly one bit

        if(labelLeft != -1 && labelRight != -1 && (grayToBinary(labelRight) == grayToBinary(labelLeft)+1)){

            int orderingRelation = (labelLeft << Nbits) + labelRight;

            // store left label column

            edges.push_back(cv::Vec4i(col-1, labelLeft, labelRight, orderingRelation));

        }

    }

    // sort

    std::sort(edges.begin(), edges.end(), sortingLarger);

    // remove duplicates

    std::vector<cv::Vec4i>::iterator it;

    it = std::unique(edges.begin(), edges.end(), sortingEqual);

    edges.resize(std::distance(edges.begin(),it));

}

static cv::Vec3b getColorSubpix(const cv::Mat& img, cv::Point2f pt){

    assert(!img.empty());

    assert(img.channels() == 3);

    int x = (int)pt.x;

    int y = (int)pt.y;

    int x0 = cv::borderInterpolate(x,   img.cols, cv::BORDER_REFLECT_101);

    int x1 = cv::borderInterpolate(x+1, img.cols, cv::BORDER_REFLECT_101);

    int y0 = cv::borderInterpolate(y,   img.rows, cv::BORDER_REFLECT_101);

    int y1 = cv::borderInterpolate(y+1, img.rows, cv::BORDER_REFLECT_101);

    float a = pt.x - (float)x;

    float c = pt.y - (float)y;

    uchar b = (uchar)cvRound((img.at<cv::Vec3b>(y0, x0)[0] * (1.f - a) + img.at<cv::Vec3b>(y0, x1)[0] * a) * (1.f - c)

                           + (img.at<cv::Vec3b>(y1, x0)[0] * (1.f - a) + img.at<cv::Vec3b>(y1, x1)[0] * a) * c);

    uchar g = (uchar)cvRound((img.at<cv::Vec3b>(y0, x0)[1] * (1.f - a) + img.at<cv::Vec3b>(y0, x1)[1] * a) * (1.f - c)

                           + (img.at<cv::Vec3b>(y1, x0)[1] * (1.f - a) + img.at<cv::Vec3b>(y1, x1)[1] * a) * c);

    uchar r = (uchar)cvRound((img.at<cv::Vec3b>(y0, x0)[2] * (1.f - a) + img.at<cv::Vec3b>(y0, x1)[2] * a) * (1.f - c)

                           + (img.at<cv::Vec3b>(y1, x0)[2] * (1.f - a) + img.at<cv::Vec3b>(y1, x1)[2] * a) * c);

    return cv::Vec3b(b, g, r);

}

void AlgorithmGrayCode::get3DPoints(SMCalibrationParameters calibration, const std::vector<cv::Mat>& frames0, const std::vector<cv::Mat>& frames1, std::vector<cv::Point3f>& Q, std::vector<cv::Vec3b>& color){

    assert(frames0.size() == N);

    assert(frames1.size() == N);

//    for(int i=0; i<1920; i++){

//        std::cout << i << " " << binaryToGray(i) << " " << grayToBinary(binaryToGray(i)) << std::endl;

//    }

    int frameRows = frames0[0].rows;

    int frameCols = frames0[0].cols;

    // rectifying homographies (rotation+projections)

    cv::Size frameSize(frameCols, frameRows);

    cv::Mat R, T;

    // stereoRectify segfaults unless R is double precision

    cv::Mat(calibration.R1).convertTo(R, CV_64F);

    cv::Mat(calibration.T1).convertTo(T, CV_64F);

    cv::Mat R0, R1, P0, P1, QRect;

    cv::stereoRectify(calibration.K0, calibration.k0, calibration.K1, calibration.k1, frameSize, R, T, R0, R1, P0, P1, QRect, 0);

//    std::cout << "R0" << std::endl << R0 << std::endl;

//    std::cout << "P0" << std::endl << P0 << std::endl;

//    std::cout << "R1" << std::endl << R1 << std::endl;

//    std::cout << "P1" << std::endl << P1 << std::endl;

    // interpolation maps

    cv::Mat map0X, map0Y, map1X, map1Y;

    cv::initUndistortRectifyMap(calibration.K0, calibration.k0, R0, P0, frameSize, CV_32F, map0X, map0Y);

    cv::initUndistortRectifyMap(calibration.K1, calibration.k1, R1, P1, frameSize, CV_32F, map1X, map1Y);

    // gray-scale and remap

    std::vector<cv::Mat> frames0Rect(N);

    std::vector<cv::Mat> frames1Rect(N);

    for(int i=0; i<N; i++){

        cv::Mat temp;

        cv::cvtColor(frames0[i], temp, CV_BayerBG2GRAY);

        cv::remap(temp, frames0Rect[i], map0X, map0Y, CV_INTER_LINEAR);

        cv::cvtColor(frames1[i], temp, CV_BayerBG2GRAY);

        cv::remap(temp, frames1Rect[i], map1X, map1Y, CV_INTER_LINEAR);

    }

//    cvtools::writeMat(frames0Rect[0], "frames0Rect_0.mat", "frames0Rect_0");

//    cvtools::writeMat(frames0[0], "frames0_0.mat", "frames0_0");

//    cvtools::writeMat(frames0Rect[22], "frames0Rect_22.mat", "frames0Rect_22");

//    cvtools::writeMat(frames0Rect[23], "frames0Rect_23.mat", "frames0Rect_23");

//    cv::imwrite("frames0[0].png", frames0[0]);

//    cv::imwrite("frames0Rect[0].png", frames0Rect[0]);

//    cv::imwrite("frames1[0].png", frames1[0]);

//    cv::imwrite("frames1Rect[0].png", frames1Rect[0]);

    // color debayer and remap

    cv::Mat color0Rect, color1Rect;

//    frames0[0].convertTo(color0Rect, CV_8UC1, 1.0/256.0);

    cv::cvtColor(frames0[0], color0Rect, CV_BayerBG2RGB);

    cv::remap(color0Rect, color0Rect, map0X, map0Y, CV_INTER_LINEAR);

//    frames1[0].convertTo(color1Rect, CV_8UC1, 1.0/256.0);

    cv::cvtColor(frames1[0], color1Rect, CV_BayerBG2RGB);

    cv::remap(color1Rect, color1Rect, map1X, map1Y, CV_INTER_LINEAR);

    int frameRectRows = frames0Rect[0].rows;

    int frameRectCols = frames0Rect[0].cols;

//cvtools::writeMat(frames0Rect[0], "frames0Rect_0.mat", "frames0Rect_0");

//cvtools::writeMat(frames0Rect[1], "frames0Rect_1.mat", "frames0Rect_1");

//cvtools::writeMat(frames0Rect[20], "frames0Rect_20.mat", "frames0Rect_20");

//cvtools::writeMat(frames0Rect[21], "frames0Rect_21.mat", "frames0Rect_21");

    // occlusion masks

    cv::Mat occlusion0Rect, occlusion1Rect;

    cv::subtract(frames0Rect[0], frames0Rect[1], occlusion0Rect);

    occlusion0Rect = (occlusion0Rect > 20) & (occlusion0Rect < 250);

    cv::subtract(frames1Rect[0], frames1Rect[1], occlusion1Rect);

    occlusion1Rect = (occlusion1Rect > 20) & (occlusion1Rect < 250);

    // erode occlusion masks

    cv::Mat strel = cv::getStructuringElement(cv::MORPH_ELLIPSE, cv::Size(2,2));

    cv::erode(occlusion0Rect, occlusion0Rect, strel);

    cv::erode(occlusion1Rect, occlusion1Rect, strel);

//cvtools::writeMat(frames0Rect[0], "frames0Rect_0.mat", "frames0Rect_0");

//cvtools::writeMat(frames0Rect[1], "frames0Rect_1.mat", "frames0Rect_1");

//cvtools::writeMat(frames0Rect[20], "frames0Rect_20.mat", "frames0Rect_20");

//cvtools::writeMat(frames0Rect[21], "frames0Rect_21.mat", "frames0Rect_21");

//    // correct for projector inversion error

//    cv::Mat W;

//    cv::add(frames0Rect[0], frames0Rect[1], W, cv::noArray(), CV_32F);

//    for(int i=2; i<N; i+=2){

//        cv::Mat S, E;

//        cv::add(frames0Rect[i], frames0Rect[i+1], S, cv::noArray(), CV_32F);

//        cv::subtract(W, S, E, cv::noArray(), CV_32F);

//        E *= 0.5;

//        cv::add(frames0Rect[i], E, frames0Rect[i], cv::noArray(), CV_16UC1);

//        cv::add(frames0Rect[i+1], E, frames0Rect[i+1], cv::noArray(), CV_16UC1);

//    }

    // correct for texture modulation and ambient

    cv::Mat A0 = frames0Rect[1];

    cv::Mat M0 = frames0Rect[0]-frames0Rect[1];

//cvtools::writeMat(A0, "A0.mat", "A0");

//cvtools::writeMat(M0, "M0.mat", "M0");

//cvtools::writeMat(frames0Rect[20], "frames0Rect_20.mat", "frames0Rect_20");

//cvtools::writeMat(frames0Rect[21], "frames0Rect_21.mat", "frames0Rect_21");

    cv::divide(256.0, M0, M0, CV_32F);

    cv::Mat A1 = frames1Rect[1];

    cv::Mat M1 = frames1Rect[0]-frames1Rect[1];

    cv::divide(256.0, M1, M1, CV_32F);

    for(int i=2; i<N; i++){

        cv::multiply(frames0Rect[i]-A0, M0, frames0Rect[i], 1.0, CV_8UC1);

        cv::multiply(frames1Rect[i]-A1, M1, frames1Rect[i], 1.0, CV_8UC1);

    }

//cvtools::writeMat(frames0Rect[22], "frames0Rect_22.mat", "frames0Rect_22");

//cvtools::writeMat(frames0Rect[23], "frames0Rect_23.mat", "frames0Rect_23");

//cvtools::writeMat(occlusion0Rect, "occlusion0Rect.mat", "occlusion0Rect");

//cvtools::writeMat(occlusion1Rect, "occlusion1Rect.mat", "occlusion1Rect");

    // decode patterns

    cv::Mat code0Rect(frameRectRows, frameRectCols, CV_32S, cv::Scalar(0));

    cv::Mat code1Rect(frameRectRows, frameRectCols, CV_32S, cv::Scalar(0));

    // into gray code

    for(int i=0; i<Nbits; i++){

        cv::Mat temp, bit0, bit1;

        cv::compare(frames0Rect[i*2+2], frames0Rect[i*2+3], temp, cv::CMP_GT);

        temp.convertTo(bit0, CV_32S, 1.0/255.0);

        cv::add(code0Rect, bit0*twopowi(Nbits-i-1), code0Rect, cv::noArray(), CV_32S);

        cv::compare(frames1Rect[i*2+2], frames1Rect[i*2+3], temp, cv::CMP_GT);

        temp.convertTo(bit1, CV_32S, 1.0/255.0);

        cv::add(code1Rect, bit1*twopowi(Nbits-i-1), code1Rect, cv::noArray(), CV_32S);

    }

//cvtools::writeMat(code0Rect, "code0Rect.mat", "code0Rect");

//cvtools::writeMat(code1Rect, "code1Rect.mat", "code1Rect");

//    // convert to standard binary

//    cv::Mat code0Binary(code0Rect.rows, code0Rect.cols, CV_32F);

//    cv::Mat code1Binary(code1Rect.rows, code1Rect.cols, CV_32F);

//    for(int r=0; r<frameRectRows; r++){

//        for(int c=0; c<frameRectCols; c++){

//            if(code0Rect.at<int>(r,c) != -1)

//                code0Binary.at<float>(r,c) = grayToBinary(code0Rect.at<int>(r,c));

//            if(code1Rect.at<int>(r,c) != -1)

//                code1Binary.at<float>(r,c) = grayToBinary(code1Rect.at<int>(r,c));

//        }

//    }

//cvtools::writeMat(code0Binary, "code0Binary.mat", "code0Binary");

//cvtools::writeMat(code1Binary, "code1Binary.mat", "code1Binary");

//    // threshold on vertical discontinuities (due to imperfect rectification)

//    cv::Mat edges0;

//    cv::Sobel(code0Binary, edges0, -1, 0, 1, 5);

//    occlusion0Rect = occlusion0Rect & (abs(edges0) < 50);

//    cv::Mat edges1;

//    cv::Sobel(code1Binary, edges1, -1, 0, 1, 5);

//    occlusion1Rect = occlusion1Rect & (abs(edges1) < 50);

//cvtools::writeMat(edges0, "edges0.mat", "edges0");

//cvtools::writeMat(edges1, "edges1.mat", "edges1");

    // set occluded pixels to -1

    for(int r=0; r<frameRectRows; r++){

        for(int c=0; c<frameRectCols; c++){

            if(occlusion0Rect.at<unsigned char>(r,c) == 0)

                code0Rect.at<int>(r,c) = -1;

            if(occlusion1Rect.at<unsigned char>(r,c) == 0)

                code1Rect.at<int>(r,c) = -1;

        }

    }

//    cvtools::writeMat(code0Rect, "code0Rect.mat", "code0Rect");

//    cvtools::writeMat(code1Rect, "code1Rect.mat", "code1Rect");

    // matching

    std::vector<cv::Vec2f> q0Rect, q1Rect;

    for(int row=0; row<frameRectRows; row++){

        // edge data structure containing [floor(column), labelLeft, labelRight, orderingRelation]

        std::vector<cv::Vec4i> edges0, edges1;

        // sorted, unique edges

        getEdgeLabels(code0Rect.row(row), Nbits, edges0);

        getEdgeLabels(code1Rect.row(row), Nbits, edges1);

        // match edges

        std::vector<cv::Vec4i> matchedEdges0, matchedEdges1;

        int i=0, j=0;

        while(i<edges0.size() && j<edges1.size()){

            if(edges0[i][3] == edges1[j][3]){

                matchedEdges0.push_back(edges0[i]);

                matchedEdges1.push_back(edges1[j]);

                i += 1;

                j += 1;

            } else if(edges0[i][3] < edges1[j][3]){

                i += 1;

            } else if(edges0[i][3] > edges1[j][3]){

                j += 1;

            }

        }

        // crude subpixel refinement

        // finds the intersection of linear interpolants in the positive/negative pattern

        for(int i=0; i<matchedEdges0.size(); i++){

            int level = Nbits - leastSignificantBitSet(matchedEdges0[i][1]^matchedEdges0[i][2]);

            // refine for camera 0

            float c0 = matchedEdges0[i][0];

            float c1 = c0+1;

            float pos0 = frames0Rect[2*level+2].at<unsigned char>(row, c0);

            float pos1 = frames0Rect[2*level+2].at<unsigned char>(row, c1);

            float neg0 = frames0Rect[2*level+3].at<unsigned char>(row, c0);

            float neg1 = frames0Rect[2*level+3].at<unsigned char>(row, c1);

            float col = c0 + (pos0 - neg0)/(neg1 - neg0 - pos1 + pos0);

            q0Rect.push_back(cv::Point2f(col, row));

            // refine for camera 1

            c0 = matchedEdges1[i][0];

            c1 = c0+1;

            pos0 = frames1Rect[2*level+2].at<unsigned char>(row, c0);

            pos1 = frames1Rect[2*level+2].at<unsigned char>(row, c1);

            neg0 = frames1Rect[2*level+3].at<unsigned char>(row, c0);

            neg1 = frames1Rect[2*level+3].at<unsigned char>(row, c1);

            col = c0 + (pos0 - neg0)/(neg1 - neg0 - pos1 + pos0);

            q1Rect.push_back(cv::Point2f(col, row));

        }

    }

    int nMatches = q0Rect.size();

    if(nMatches < 1){

        Q.resize(0);

        color.resize(0);

        return;

    }

    // retrieve color information (at integer coordinates)

    color.resize(nMatches);

    for(int i=0; i<nMatches; i++){

        cv::Vec3b c0 = color0Rect.at<cv::Vec3b>(q0Rect[i][1], q0Rect[i][0]);

        cv::Vec3b c1 = color1Rect.at<cv::Vec3b>(q1Rect[i][1], q1Rect[i][0]);

//        cv::Vec3b c0 = getColorSubpix(color0Rect, q0Rect[i]);

//        cv::Vec3b c1 = getColorSubpix(color1Rect, q0Rect[i]);

        color[i] = 0.5*c0 + 0.5*c1;

    }

    // triangulate points

    cv::Mat QMatHomogenous, QMat;

//    cv::Mat C0 = P0.clone();

//    cv::Mat C1 = P1.clone();

//    C0.colRange(0, 3) = C0.colRange(0, 3)*R0;

//    C1.colRange(0, 3) = C1.colRange(0, 3)*R1.t();

    cv::triangulatePoints(P0, P1, q0Rect, q1Rect, QMatHomogenous);

    cvtools::convertMatFromHomogeneous(QMatHomogenous, QMat);

    // undo rectifying rotation

    cv::Mat R0Inv;

    cv::Mat(R0.t()).convertTo(R0Inv, CV_32F);

    QMat = R0Inv*QMat;

    cvtools::matToPoints3f(QMat, Q);

}