It is shown that the covariance operator of a locally stationary process has approximate eigenvectors that are local cosine functions. We model locally stationary processes with pseudo-differential operators that are time-varying convolutions. An adaptive covariance estimation is calculated by searching first for a "best" local cosine basis which approximates the covariance by a band or a diagonal matrix. The estimation is obtained from regularized versions of the diagonal coefficients in the best basis.