How to estimate the 3D power spectrum of the Lyman-$\alpha$ forest

We derive and numerically implement an algorithm for estimating the 3D power spectrum of the Lyman-$\alpha$ (Ly-$\alpha$) forest flux fluctuations. The algorithm exploits the unique geometry of Ly-$\alpha$ forest data to efficiently measure the cross-spectrum between lines of sight as a function of parallel wavenumber, transverse separation and redshift. The key to fast evaluation is to approximate the global covariance matrix as block-diagonal, where only pixels from the same spectrum are correlated. We then compute the eigenvectors of the derivative of the signal covariance with respect to cross-spectrum parameters, and project the inverse-covariance-weighted spectra onto them. This acts much like a radial Fourier transform over redshift windows. The resulting cross-spectrum inference is then converted into our final product, an approximation of the likelihood for the 3D power spectrum expressed as second order Taylor expansion around a fiducial model. We demonstrate the accuracy and scalability of the algorithm and comment on possible extensions. Our algorithm will allow efficient analysis of the upcoming Dark Energy Spectroscopic Instrument dataset.