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Prosilica Stereo Calibration Epipolar error hardware sync


We are trying to calibrate stereo prosilica gige manta cameras which have a hardware sync setup to trigger master/slave. We tried to modify the driver to send the slave the timestamp of the master to sync the timestamps in addition. We try to stereo calibrate it and the epipolar error is unstable from .5 -> 10. We believe this is causing a disparity map that isn't able to match everything it sees very well, especially close objects. Any thoughts on properly creating an exact sync or reducing the epipolar error?