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It looks like you put in a 90 degree yaw at the top. Note that you used the fixed axis RPY method.

It looks like you put in a 90 degree yaw at the top. Note that you used the fixed axis RPY method.

That is the right method and the right output. With the euler angle conventions used here(ZYX) yaw is evaluated first, thus a transform of a yaw only will only effect the yaw terms. Your assertion that pitch becomes roll only happens if you don't change your reference frame after applying the transformation. But transformQuaternion puts you into base_link coordinate frame.