Stereo rectification

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Hi,

Could someone offer me some advise on the following problems.

I have a stereo setup and I am able to stereo rectify the chessborad images during calibrations. When I then use the same remap values to remap real world images they are not row aligned after I call stereorectify.

I have taken over 80 pairs of chessboard images and the error is less than 1. The rectified calibrated images (chessboard) all look correctly rectified good but I can't figure out why the normal images are not rectifying. I'm using the same code for both.

I use stereocalibrate and stereorectify as the two main functions and R, T R1 R2 P1 P2 are identical for both tests

I hope this makes sense

Thanks