A method is proposed to calculate the space-dependent coefficient of diffusion and chemical potential occurring in the Fokker-Planck equation for diffusion in heterogeneous media. These quantities are extracted from a set of population decays for point sources at chosen locations in the medium to be tested. Numerical stability and consistency of the method are demonstrated. This method provides a direct link between short-time molecular dynamics simulations and long-time Fokker-Planck type calculations.