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When using the camera_calibration package for stereo camera calibration the images of right and left camera are rectified and adjusted to become "ideal" stereo images. That means that corresponding points in left and right image have the same value in y (i.e. the epipoles are infinite, epipolar lines are parallel to the x-axis).
In this setting, no fundamental matrix but the baseline (distance from left to right camera center) is needed for 3D triangulation. This information is found in the CameraInfo message of the right camera. Please have a look at the CameraInfo message and at corresponding documentation.
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