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I'm setting up a stereo camera system (with two cameras). I'm trying to get rotation matrix and translation vector with OpenCV in c++. I have computed matrix camera and distortion vector for each camera using cameraCalibrate opencv function. Now I'm trying to calculate rotation matrix and translation vector using stereoCalibrate. I did not understand the stereoCalibrate parametes: imagePoints1 and imagePoints2. Have these two parameters contain the same point in the same scene viewed by the two cameras or can I detect different points from the same scene taken by the cameras?

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The goal if stereo calibration is to gather information about the position of the same object on two images. Taking into consideration points belonging to different objects does not make any sense in stereoCalibrate. That's also what documentation clearly says. In other words, you should pass there "the same points viewed by two cameras".