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//
// Gray Code Structured Light with horizontal and vertical encoding
//
// This implementation of Gray encoding uses horizontal and vertial stripes, which adds some encoding redundancy, but avoids interpolation effects from rectifying homographies.
//

#include "AlgorithmGrayCodeHorzVert.h"
#include <cmath>
#include <assert.h>
#include "cvtools.h"
#include "algorithmtools.h"

// Algorithm
AlgorithmGrayCodeHorzVert::AlgorithmGrayCodeHorzVert(unsigned int _screenCols, unsigned int _screenRows) : Algorithm(_screenCols, _screenRows){

    NbitsHorz = ceilf(log2f((float)screenCols));
    NbitsVert =  ceilf(log2f((float)screenRows));
    N = 2 + (NbitsHorz+NbitsVert)*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<NbitsHorz; 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, NbitsHorz-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);
    }

    // vertical encoding patterns
    for(unsigned int p=0; p<NbitsVert; p++){
        cv::Mat pattern(screenRows, 1, CV_8UC3);
        cv::Mat patternInv(screenRows, 1, CV_8UC3);

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

            unsigned int jGray = binaryToGray(j);
            // Amplitude of channels
            int bit = (int)getBit(jGray, NbitsVert-p);
            pattern.at<cv::Vec3b>(j,0) = cv::Vec3b(255.0*bit,255.0*bit,255.0*bit);
            int invBit = bit^1;
            patternInv.at<cv::Vec3b>(j,0) = cv::Vec3b(255.0*invBit,255.0*invBit,255.0*invBit);
        }
        patterns.push_back(pattern);
        patterns.push_back(patternInv);
    }

}

cv::Mat AlgorithmGrayCodeHorzVert::getEncodingPattern(unsigned int depth){
    return patterns[depth];
}


typedef struct intersection{
    unsigned int row;
    unsigned int col;
    // 64 bit integer (long long)
    unsigned long id;
    intersection() : row(0), col(0), id(0){}
    intersection(unsigned int _row, unsigned int _col, unsigned long long _id) :
        row(_row), col(_col), id(_id){}
} intersection;


static bool sortingLarger(intersection i,intersection j){ return (i.id<j.id);}
static bool sortingEqual(intersection i,intersection j){ return (i.id==j.id);}

static void getIntersectionLabels(const cv::Mat& codeHorz, const cv::Mat& codeVert, const int NbitsHorz, const int NbitsVert, std::vector<intersection>& intersections){

    int nRows = codeHorz.rows;
    int nCols = codeHorz.cols;

    int labelHorz;
    int labelVert;
    int labelHorzRight;
    int labelVertBelow;

    // collect intersections
    for(int row=0; row<nRows-1; row++){
        for(int col=0; col<nCols-1; col++){

            labelHorz = codeHorz.at<int>(row, col);
            labelHorzRight = codeHorz.at<int>(row, col+1);

            labelVert = codeVert.at<int>(row, col);
            labelVertBelow = codeVert.at<int>(row+1, col);

            // labels need to be non-background, and differ in exactly one bit
            if(labelHorz != -1 && labelHorzRight != -1 &&
               (grayToBinary(labelHorzRight) == grayToBinary(labelHorz)+1) &&
               labelVert != -1 && labelVertBelow != -1 &&
               (grayToBinary(labelVertBelow) == grayToBinary(labelVert)+1)){

                // shift together labels to form unique intersection id
                unsigned long id = ((ulong)labelHorz << (NbitsHorz+2*NbitsVert)) + ((ulong)labelHorzRight << (2*NbitsVert)) +
                                   ((ulong)labelVert << NbitsVert) + (ulong)labelVertBelow;

                // store intersection
                intersections.push_back(intersection(row, col, id));
            }
        }
    }
    // sort
    std::sort(intersections.begin(), intersections.end(), sortingLarger);

    // remove duplicates
    std::vector<intersection>::iterator it;
    it = std::unique(intersections.begin(), intersections.end(), sortingEqual);
    intersections.resize(std::distance(intersections.begin(),it));
}

static void getSubpixelCoordinates(const std::vector<intersection>& matches, const std::vector<cv::Mat>& frames, const int NbitsHorz, const int NbitsVert, std::vector<cv::Point2f> &q){

    int nMatches = matches.size();
    q.resize(nMatches);

    // subpixel refinement finds the intersection of linear interpolants in the positive/negative pattern
    for(int i=0; i<nMatches; i++){

        // shift the labels back out from id
        int labelHorz = (matches[i].id >> (NbitsHorz+2*NbitsVert)) & ((1 << NbitsHorz) - 1);
        int labelHorzRight = (matches[i].id >> (2*NbitsVert)) & ((1 << NbitsHorz) - 1);
        int labelVert = (matches[i].id >> NbitsVert) & ((1 << NbitsVert) - 1);
        int labelVertBelow = matches[i].id  & ((1 << NbitsVert) - 1);

//        std::cout << "id: " << matches[i].id << std::endl;
//        std::cout << "labelHorz: " << labelHorz << std::endl;
//        std::cout << "labelHorzRight: " << labelHorzRight << std::endl;
//        std::cout << "labelVert: " << labelVert << std::endl;
//        std::cout << "labelVertBelow: " << labelVertBelow << std::endl;

        // determine the levels at which the edges exists
        int levelHorz = NbitsHorz - leastSignificantBitSet(labelHorz^labelHorzRight);
        int levelVert = NbitsVert - leastSignificantBitSet(labelVert^labelVertBelow);

        // interpolate horizontal coordinate
        float row = matches[i].row;
        float col = matches[i].col;
        float colRight = col+1;

        float posHorz = frames[2*levelHorz+2].at<unsigned char>(row, col);
        float negHorz = frames[2*levelHorz+3].at<unsigned char>(row, col);
        float posHorzRight = frames[2*levelHorz+2].at<unsigned char>(row, colRight);
        float negHorzRight = frames[2*levelHorz+3].at<unsigned char>(row, colRight);

        float x = col + (posHorz - negHorz)/(negHorzRight - negHorz - posHorzRight + posHorz);

        // interpolate vertical coordinate
        float rowBelow = row+1;

        float posVert = frames[2*NbitsHorz+2*levelVert+2].at<unsigned char>(row, col);
        float negVert = frames[2*NbitsHorz+2*levelVert+3].at<unsigned char>(row, col);
        float posVertBelow = frames[2*NbitsHorz+2*levelVert+2].at<unsigned char>(rowBelow, col);
        float negVertBelow = frames[2*NbitsHorz+2*levelVert+3].at<unsigned char>(rowBelow, col);

        float y = row + (posVert - negVert)/(negVertBelow - negVert - posVertBelow + posVert);

        // write into return vector
        q[i] = cv::Point2f(x, y);

    }
}

void AlgorithmGrayCodeHorzVert::get3DPoints(const 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);

    int frameRows = frames0[0].rows;
    int frameCols = frames0[0].cols;

    // gray-scale
    std::vector<cv::Mat> frames0Gray(N);
    std::vector<cv::Mat> frames1Gray(N);
    for(unsigned int i=0; i<N; i++){
        cv::cvtColor(frames0[i], frames0Gray[i], CV_BayerBG2GRAY);
        cv::cvtColor(frames1[i], frames1Gray[i], CV_BayerBG2GRAY);
    }

    // colors
    cv::Mat color0;
//    frames0[0].convertTo(color0, CV_8UC3, 1.0/256.0);
    cv::cvtColor(frames0[0], color0, CV_BayerBG2RGB);
    cv::Mat color1;
//    frames1[0].convertTo(color1, CV_8UC3, 1.0/256.0);
    cv::cvtColor(frames1[0], color1, CV_BayerBG2RGB);

    // occlusion masks
    cv::Mat occlusion0, occlusion1;
    cv::subtract(frames0[0], frames0[1], occlusion0);
    occlusion0 = (occlusion0 > 20) & (occlusion0 < 250);
    cv::subtract(frames1[0], frames1[1], occlusion1);
    occlusion1 = (occlusion1 > 20) & (occlusion1 < 250);

//    // erode occlusion masks
//    cv::Mat strel = cv::getStructuringElement(cv::MORPH_ELLIPSE, cv::Size(3,3));
//    cv::erode(occlusion0, occlusion0, strel);
//    cv::erode(occlusion1, occlusion1, strel);

//cvtools::writeMat(occlusion0, "occlusion0.mat", "occlusion0");
//cvtools::writeMat(occlusion1, "occlusion1.mat", "occlusion1");

    // decode patterns
    cv::Mat code0Horz(frameRows, frameCols, CV_32S, cv::Scalar(0));
    cv::Mat code1Horz(frameRows, frameCols, CV_32S, cv::Scalar(0));
    cv::Mat code0Vert(frameRows, frameCols, CV_32S, cv::Scalar(0));
    cv::Mat code1Vert(frameRows, frameCols, CV_32S, cv::Scalar(0));

    // horizontal codes into gray code
    for(unsigned int i=0; i<NbitsHorz; i++){
        cv::Mat bit0;
        cv::compare(frames0Gray[i*2+2], frames0Gray[i*2+3], bit0, cv::CMP_GT);
        bit0.convertTo(bit0, CV_32S, 1.0/255.0);
        cv::add(code0Horz, bit0*twopowi(NbitsHorz-i-1), code0Horz, cv::Mat(), CV_32S);

        cv::Mat bit1;
        cv::compare(frames1Gray[i*2+2], frames1Gray[i*2+3], bit1, cv::CMP_GT);
        bit1.convertTo(bit1, CV_32S, 1.0/255.0);
        cv::add(code1Horz, bit1*twopowi(NbitsHorz-i-1), code1Horz, cv::Mat(), CV_32S);
    }

    // vertical codes into gray code
    for(unsigned int i=0; i<NbitsVert; i++){
        cv::Mat bit0;
        cv::compare(frames0Gray[i*2+2*NbitsHorz+2], frames0Gray[i*2+2*NbitsHorz+3], bit0, cv::CMP_GT);
        bit0.convertTo(bit0, CV_32S, 1.0/255.0);
        cv::add(code0Vert, bit0*twopowi(NbitsVert-i-1), code0Vert, cv::Mat(), CV_32S);

        cv::Mat bit1;
        cv::compare(frames1Gray[i*2+2*NbitsHorz+2], frames1Gray[i*2+2*NbitsHorz+3], bit1, cv::CMP_GT);
        bit1.convertTo(bit1, CV_32S, 1.0/255.0);
        cv::add(code1Vert, bit1*twopowi(NbitsVert-i-1), code1Vert, cv::Mat(), CV_32S);
    }

    // set occluded pixels to -1
    for(int r=0; r<frameRows; r++){
        for(int c=0; c<frameCols; c++){
            if(occlusion0.at<char>(r,c) == 0){
                code0Horz.at<int>(r,c) = -1;
                code0Vert.at<int>(r,c) = -1;
            }
            if(occlusion1.at<char>(r,c) == 0){
                code1Horz.at<int>(r,c) = -1;
                code1Vert.at<int>(r,c) = -1;
            }
        }
    }

//    cvtools::writeMat(code0Horz, "code0Horz.mat", "code0Horz");
//    cvtools::writeMat(code1Horz, "code1Horz.mat", "code1Horz");
//    cvtools::writeMat(code0Vert, "code0Vert.mat", "code0Vert");
//    cvtools::writeMat(code1Vert, "code1Vert.mat", "code1Vert");

    // get intersections
    std::vector<intersection> intersections0, intersections1;
    getIntersectionLabels(code0Horz, code0Vert, NbitsHorz, NbitsVert, intersections0);
    getIntersectionLabels(code1Horz, code1Vert, NbitsHorz, NbitsVert, intersections1);

    // match intersections
    std::vector<intersection> matches0, matches1;
    unsigned int i=0, j=0;

    while(i<intersections0.size() && j<intersections1.size()){
        if(intersections0[i].id == intersections1[j].id){
            matches0.push_back(intersections0[i]);
            matches1.push_back(intersections1[j]);
            i += 1;
            j += 1;
        } else if(intersections0[i].id < intersections1[j].id){
            i += 1;
        } else if(intersections0[i].id > intersections1[j].id){
            j += 1;
        }
    }

    int nMatches = matches0.size();

    if(nMatches < 1){
        Q.resize(0);
        color.resize(0);

        return;
    }

    std::vector<cv::Point2f> q0(nMatches), q1(nMatches);

//    for(int i=0; i<nMatches; i++){
//        q0[i] = cv::Point2f(matches0[i].col, matches0[i].row);
//        q1[i] = cv::Point2f(matches1[i].col, matches1[i].row);
//    }

    // subpixel refinement
    getSubpixelCoordinates(matches0, frames0Gray, NbitsHorz, NbitsVert, q0);
    getSubpixelCoordinates(matches1, frames1Gray, NbitsHorz, NbitsVert, q1);

    // retrieve color information (at subpixel coordinates)
    color.resize(nMatches);
    for(int i=0; i<nMatches; i++){
        cv::Vec3b c0 = color0.at<cv::Vec3b>(std::floor(q0[i].y), std::floor(q0[i].x));
        cv::Vec3b c1 = color1.at<cv::Vec3b>(std::floor(q1[i].y), std::floor(q1[i].x));

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

    //cv::correctMatches(calibration.F, q0, q1, q0, q1);
    // correct for lens distortion
    cv::undistortPoints(q0, q0, calibration.K0, calibration.k0, cv::noArray(), calibration.K0);
    cv::undistortPoints(q1, q1, calibration.K1, calibration.k1, cv::noArray(), calibration.K1);
    cv::correctMatches(calibration.F, q0, q1, q0, q1);

    // Triangulate points
    cv::Mat P0(3, 4, CV_32F, cv::Scalar(0.0));
    cv::Mat(calibration.K0).copyTo(P0.colRange(0, 3));

    cv::Mat P1(3, 4, CV_32F), temp(3,4,CV_32F);
    cv::Mat(calibration.R1).copyTo(temp(cv::Range(0,3), cv::Range(0,3)));
    cv::Mat(calibration.T1).copyTo(temp(cv::Range(0,3), cv::Range(3,4)));
    P1 = cv::Mat(calibration.K1) * temp;

    cv::Mat QMatHomogenous, QMat;
    cv::triangulatePoints(P0, P1, q0, q1, QMatHomogenous);

    cvtools::convertMatFromHomogeneous(QMatHomogenous, QMat);
    cvtools::matToPoints3f(QMat, Q);

}