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VideoCapture from CSI camera is way off

I am using OpenCV 3.1 with CUDA enabled on the Tegra K1 with the OV5640 CSI Camera.

I tried for a long time to get Gstreamer working with VideoCapture to no avail. I tried multiple different pipelines and not one of them managed to open the camera so I used the default VideoCapture constructor. My code is as follows:

    cv::VideoCapture cap(0);
if (!cap.isOpened()){
    printf("Camera not opened \n");
    return -1;

// View video
cv::Mat frame;

for(int i = 0; i < 1500; i++) {

    cap >> frame;

    imshow("Display window", frame);



and my output is as follows: image description

At first, I thought it was the Bayer output but after some investigating the image stream has the following properties: 640x480 resolution

3-channel image

CV_16U3 - 16 bit encoding

Since I do not know the colorspace the image is in, I tried to convert to every possible colorspace with cvtColor() and every transformation ended up making the image worse.

Any help would be greatly appreciated. I was initially trying to get the images in YUV or YCrCb colorspace but HSV or LAB would also work just fine.