OpenCV: Merge separated JPEG bayer channels - opencv

Question

I have a camera that is giving 4 separated JPEG images for the 4 different Bayer channels (B,G1,G2,R).
I want to transform this in to a colour image.
What I'm doing at the moment is uncompress the jpeg, restore the "original" image manually and converting to a colour image using cvtColor. But this is too slow. How could I do it better?
cv::Mat imgMat[4]=cv::Mat::zeros(616, 808, CV_8U); //height, width
for (k=0;k<4;k++) {
........
imgMat[k] = cv::imdecode(buffer, CV_LOAD_IMAGE_GRAYSCALE);
}
//Reconstruct the original image from the four channels! RGGB
cv::Mat Reconstructed=cv::Mat::zeros(1232, 1616, CV_8U);
int x,y;
for(x=0;x<1616;x++){
for(y=0;y<1232;y++){
if(y%2==0){
if(x%2==0){
//R
Reconstructed.at<uint8_t>(y,x)=imgMat[0].at<uint8_t>(y/2,x/2);
}
else{
//G1
Reconstructed.at<uint8_t>(y,x)=imgMat[1].at<uint8_t>(y/2,floor(x/2));
}
}
else{
if(x%2==0){
//G2
Reconstructed.at<uint8_t>(y,x)=imgMat[2].at<uint8_t>(floor(y/2),x/2);
}
else{
//B
Reconstructed.at<uint8_t>(y,x)=imgMat[3].at<uint8_t>(floor(y/2),floor(x/2));
}
}
}
}
//Debayer
cv::Mat ReconstructedColor;
cv::cvtColor(Reconstructed, ReconstructedColor, CV_BayerBG2BGR);
It seems clear that what it takes more time is decoding the jpeg images. Has somebody some advice/trick I could use to speed up this code?

Answer 1

Firstly you should do a profile to see where the time is mostly going. Maybe it is all in imdecode(), as "seems clear", but you might be wrong.
If not, .at<>() is a bit slow (and you are calling it nearly 4 million times). You can get some speedup by more efficent scanning of the image. Also you do not need floor() - that will avoid converting an int to double and back again (2 million times). Something like this will be faster:
int x , y;
for(y = 0; y < 1232; y++){
uint8_t* row = Reconstructed.ptr<uint8_t>(y);
if(y % 2 == 0){
uint8_t* i0 = imgMat[0].ptr<uint8_t>(y / 2);
uint8_t* i1 = imgMat[1].ptr<uint8_t>(y / 2);
for(x = 0; x < 1616; ){
//R
row[x] = i0[x / 2];
x++;
//G1
row[x] = i1[x / 2];
x++;
}
}
else {
uint8_t* i2 = imgMat[2].ptr<uint8_t>(y / 2);
uint8_t* i3 = imgMat[3].ptr<uint8_t>(y / 2);
for(x = 0; x < 1616; ){
//G2
row[x] = i2[x / 2];
x++;
//B
row[x] = i3[x / 2];
x++;
}
}
}